{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30662576", "kind": "science-record", "revision": 7, "content_hash": "sha256:d4f49ff5749dbd049b02aebe7f63cd1f234b08ee00e3ba257e22da2694d351dd", "created_at": "2026-11-01T15:40:40Z", "updated_at": "2026-11-01T22:00:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Core Gene Biomarkers in Patients with Diabetic Cardiomyopathy.", "doi": "10.1155/2018/6025061", "pmid": "30662576", "authors": ["Ning Li", "Haiming Wu", "Rongxin Geng", "Qizhu Tang"], "journal": "Disease markers", "year": 2018, "abstract": "Diabetic cardiomyopathy (DCM) is a disorder of the myocardium in diabetic patients, which is one of the critical complications of diabetes giving rise to an increased mortality. However, the underlying mechanisms of DCM remain incompletely understood presently. This study was designed to screen the potential molecules and pathways implicated with DCM. GSE26887 involving 5 control individuals and 7 DCM patients was selected from the GEO database to identify the differentially expressed genes (DEGs). DAVID was applied to perform gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. A protein-protein interaction (PPI) network was also constructed to visualize the interactions among these DEGs. To further validate significant genes and pathways, quantitative real-time PCR (qPCR) and Western blot were performed. A total of 236 DEGs were captured, including 134 upregulated and 102 downregulated genes. GO, KEGG, and the PPI network disclosed that inflammation, immune disorders, metabolic disturbance, and mitochondrial dysfunction were significantly enriched in the development of DCM. Notably, IL6 was an upregulated hub gene with the highest connectivity degree, suggesting that it may interact with a great many molecules and pathways. Meanwhile, SOCS3 was also one of the top 15 hub genes in the PPI network. Herein, we detected the protein level of STAT3 and SOCS3 in a mouse model with DCM. Western blot results showed that the protein level of SOCS3 was significantly lower while phosphorylated-STAT3 (P-STAT3) was activated in mice with DCM. In vitro results also uncovered the similar alterations of SOCS3 and P-STAT3 in cardiomyocytes and cardiac fibroblasts induced by high glucose (HG). However, overexpression of SOCS3 could significantly reverse HG-induced cardiomyocyte hypertrophy and collagen synthesis of cardiac fibroblasts. Taken together, our analysis unveiled potential biomarkers and molecular mechanisms in DCM, which could be helpful to the diagnosis and treatment of DCM.", "claims": [{"id": "claim-method", "statement": "The obtained data were presented as mean ± SD (standard deviation) and assessed by the two-tailed Student's t-test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30662576", "locator": "sections[11] \"2.9. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE26887"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE26887"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30662576", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2018/6025061", "sha256": "sha256:bd2a9386b529e4da3f7e150655046d6bc36d3ec1a7b82fa57301b5a20e9a7b5d", "bytes": 48350, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2018/6025061", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6313979", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE26887", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26887", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26887", "version": null, "note": "The data used to support the findings of this study are available from the corresponding author upon request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study are available from the corresponding author upon request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM662158", "GSM662159", "GSM662160", "GSM662161", "GSM662162", "GSM662163", "GSM662164", "GSM662165", "GSM662166", "GSM662167", "GSM662168", "GSM662169", "GSM662170", "GSM662171", "GSM662172", "GSM662173", "GSM662174", "GSM662175", "GSM662176", "GSM662177", "GSM662178", "GSM662179", "GSM662180", "GSM662181"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Transcriptome analysis of diabetic and non diabetic patients affected by post-ischemic heart failure", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30662576:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:b7b3b7e7e6bc4a67d966690d4956b67960db2c3c7df96773298171b4cbdbdc01", "bytes": 1200, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#tab1", "version": null, "note": "The top 5 upregulated and downregulated differentially expressed genes in patients with diabetic cardiomyopathy.", "structure": {"pmcid": "PMC6313979", "section_index": 13, "section_title": "3.1. Identification of DEGs", "row_count": 12, "column_count": 5}, "table": {"label": "Table 1", "caption": "The top 5 upregulated and downregulated differentially expressed genes in patients with diabetic cardiomyopathy.", "rows": [["DEGs", "Gene title", "Gene symbol", "LogFC", "Biological function"], ["Upregulated", "Natriuretic peptide A", "NPPA", "3.53", "Extracellular fluid volume and electrolyte homeostasis"], ["Secreted frizzled related protein 4", "SFRP4", "2.71", "Soluble modulators of Wnt signaling"], ["Desmocollin 1", "DSC1", "2.44", "Calcium-dependent glycoprotein"], ["Nebulin", "NEB", "2.4", "Cytoskeleton"], ["Frizzled-related protein", "FRZB", "2.36", "Soluble modulators of Wnt signaling"], [""], ["Downregulated", "Serpin family E member 1", "SERPINE1", "−2.48", "Inhibitor of fibrinolysis"], ["Serpin family A member 3", "SERPINA3", "−2.44", "Anti-inflammatory and antioxidant effects"], ["Ankyrin repeat domain 2", "ANKRD2", "−2.16", "Modulator of NF-κB-mediated inflammatory"], ["X-ray repair cross-complementing 4", "XRCC4", "−2.05", "DNA repair"], ["S100 calcium-binding protein A8", "S100A8", "−1.98", "Regulating inflammation and oxidative stress, activatingTLR4 signaling"]], "row_count": 12, "column_count": 5, "numeric_cells": 18, "header_rows": 1, "locator": "section[13]/table-wrap[1]#tab1"}}, {"id": "asset:table:pmid:30662576:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:d5cced7b3388f6a929678d58c2136b2b1972dfd9a7fd0f0a1f7ce75a164781cc", "bytes": 2378, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#tab2", "version": null, "note": "Gene ontology analysis of differentially expressed genes in patients with diabetic cardiomyopathy.", "structure": {"pmcid": "PMC6313979", "section_index": 14, "section_title": "3.2. GO Enrichment Analysis", "row_count": 32, "column_count": 5}, "table": {"label": "Table 2", "caption": "Gene ontology analysis of differentially expressed genes in patients with diabetic cardiomyopathy.", "rows": [["Expression", "Category", "Term", "Count", "%"], ["Upregulated", "GOTERM_BP_DIRECT", "GO:0035589~G-protein-coupled purinergic nucleotide receptor signaling pathway", "9", "0.05"], ["GOTERM_BP_DIRECT", "GO:0007155~fatty acid metabolism", "8", "0.05"], ["GOTERM_BP_DIRECT", "GO:0001501~mitochondrial membrane potential", "6", "0.04"], ["GOTERM_BP_DIRECT", "GO:0030198~extracellular matrix organization", "6", "0.04"], ["GOTERM_BP_DIRECT", "GO:0007409~mitochondrial permeability transition", "5", "0.03"], ["GOTERM_CC_DIRECT", "GO:0016021~integral component of membrane", "42", "0.25"], ["GOTERM_CC_DIRECT", "GO:0005886~plasma membrane", "37", "0.22"], ["GOTERM_CC_DIRECT", "GO:0070062~extracellular exosome", "29", "0.17"], ["GOTERM_CC_DIRECT", "GO:0005615~extracellular space", "22", "0.13"], ["GOTERM_CC_DIRECT", "GO:0005576~extracellular region", "20", "0.11"], ["GOTERM_MF_DIRECT", "GO:0008270~glucose transporter", "13", "0.08"], ["GOTERM_MF_DIRECT", "GO:0005509~calcium ion binding", "11", "0.07"], ["GOTERM_MF_DIRECT", "GO:0008201~heparin binding", "7", "0.05"], ["GOTERM_MF_DIRECT", "GO:0005518~collagen binding", "5", "0.03"], ["GOTERM_MF_DIRECT", "GO:0050661~NADP binding", "4", "0.03"], [""], ["Downregulated", "GOTERM_BP_DIRECT", "GO:0006954~inflammatory response", "11", "0.07"], ["GOTERM_BP_DIRECT", "GO:0008284~lipid intake", "9", "0.06"], ["GOTERM_BP_DIRECT", "GO:0042493~response to drug", "6", "0.04"], ["GOTERM_BP_DIRECT", "GO:0006955~immune response", "6", "0.04"], ["GOTERM_BP_DIRECT", "GO:0002576~platelet degranulation", "5", "0.04"], ["GOTERM_CC_DIRECT", "GO:0005886~plasma membrane", "31", "0.21"], ["GOTERM_CC_DIRECT", "GO:0005615~extracellular space", "23", "0.15"], ["GOTERM_CC_DIRECT", "GO:0005576~extracellular region", "21", "0.14"], ["GOTERM_CC_DIRECT", "GO:0070062~extracellular exosome", "21", "0.14"], ["GOTERM_CC_DIRECT", "GO:0005789~endoplasmic reticulum membrane", "13", "0.09"], ["GOTERM_MF_DIRECT", "GO:0005515~protein binding", "58", "0.39"], ["GOTERM_MF_DIRECT", "GO:0008083~mitochondrial uncoupling", "5", "0.03"], ["GOTERM_MF_DIRECT", "GO:0005125~cytokine activity", "5", "0.03"], ["GOTERM_MF_DIRECT", "GO:0003779~actin binding", "5", "0.03"], ["GOTERM_MF_DIRECT", "GO:0016791~phosphatase activity", "3", "0.03"]], "row_count": 32, "column_count": 5, "numeric_cells": 90, "header_rows": 1, "locator": "section[14]/table-wrap[1]#tab2"}}, {"id": "asset:table:pmid:30662576:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0995fc600241ffd45c1db0b7d886a430bbf814692b9ab91d60913406dfa1dcfb", "bytes": 915, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[1]#tab3", "version": null, "note": "KEGG pathway analysis of differentially expressed genes in patients with diabetic cardiomyopathy.", "structure": {"pmcid": "PMC6313979", "section_index": 15, "section_title": "3.3. 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PPI Analysis", "row_count": 16, "column_count": 3}, "table": {"label": "Table 4", "caption": "Top 15 hub genes with higher degree of connectivity.", "rows": [["Gene", "Degree of connectivity", "P value"], ["IL6", "29", "5.48E − 04"], ["MYC", "17", "3.99E − 03"], ["ACTA2", "14", "9.78E − 06"], ["SERPINE1", "14", "1.16E − 02"], ["ASPN", "12", "9.15E − 03"], ["SPP1", "11", "4.04E − 02"], ["KIT", "11", "4.54E − 03"], ["TFRC", "9", "3.34E − 04"], ["FMOD", "9", "3.42E − 04"], ["PDE5A", "9", "2.96E − 04"], ["MYH6", "8", "1.55E − 03"], ["FPR1", "8", "1.71E − 06"], ["C3", "7", "1.18E − 02"], ["CDKN1A", "7", "3.94E − 04"], ["SOCS3", "7", "1.02E − 03"]], "row_count": 16, "column_count": 3, "numeric_cells": 30, "header_rows": 1, "locator": "section[16]/table-wrap[1]#tab4"}}, {"id": "asset:table:pmid:30662576:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:04aba451e7cfd98eacffea5b3e79f2b6bac698500e17951cb4b1bda774aa5dc7", "bytes": 1358, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[2]#tab5", "version": null, "note": "Gene-specific primers used in quantitative real-time PCR.", "structure": {"pmcid": "PMC6313979", "section_index": 16, "section_title": "3.4. PPI Analysis", "row_count": 30, "column_count": 4}, "table": {"label": "Table 5", "caption": "Gene-specific primers used in quantitative real-time PCR.", "rows": [["Species", "Genes", "", "Sequences"], ["Mouse", "GAPDH", "Forward", "5′-ACTCCACTCACGGCAAATTC-3′"], ["Reverse", "5′-TCTCCATGGTGGTGAAGACA-3′"], [""], ["Mouse", "NPPA", "Forward", "5′-CCCTCCGATAGATCTGCCCT-3′"], ["Reverse", "5′-GTCAATCCTACCCCCGAAGC-3′"], [""], ["Mouse", "SFRP4", "Forward", "5′-AAAAGCCGTCCAGAGGAGTG-3′"], ["Reverse", "5′-GAGGGACTTGTGTTCGAGGG-3′"], [""], ["Mouse", "DSC31", "Forward", "5′-GATCAGGCCAGTGGAAATGT-3′"], ["Reverse", "5′-GTGTGTTTCGTGCAACCATC-3′"], [""], ["Mouse", "NEB", "Forward", "5′-ATCCTGTCCAAACTAAGGCTCG-3′"], ["Reverse", "5′-ACCTCTTTAGCATAGTAGTCCGC-3′"], [""], ["Mouse", "SERPINE1", "Forward", "5′-GGGTTCACTTTACCCCTCCG-3′"], ["Reverse", "5′-TAGGGCAGTTCCACAACGTC-3′"], [""], ["Mouse", "SERPINA3", "Forward", "5′-TGACCTTTCTCAGCACGACC-3′"], ["Reverse", "5′-AATAGGGGAGGATGGGAGCA-3′"], [""], ["Mouse", "ANKRD2", "Forward", "5′-TTGCCCAGGAGGAAGAGACT-3′"], ["Reverse", "5′-TGTCTCTCACGTTGGTGTCG-3′"], [""], ["Mouse", "XRCC4", "Forward", "5′-TTGGGCGCATCGGTTTATCT-3′"], ["Reverse", "5′-ACCAGTGCCTTTCTCAGCTC-3′"], [""], ["Mouse", "S100A8", "Forward", "5′-TTCGTGACAATGCCGTCTGA-3′"], ["Reverse", "5′-GGCCAGAAGCTCTGCTACTC-3′"]], "row_count": 30, "column_count": 4, "numeric_cells": 22, "header_rows": 1, "locator": "section[16]/table-wrap[2]#tab5"}}], "gaps": ["asset:data:geo:GSE26887 not downloaded", "asset:data:geo:GSE26887 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "student_t_test", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["student_t"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The obtained data were presented as mean ± SD (standard deviation) and assessed by the two-tailed Student's t-test."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": ["method.student_t"]}, "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": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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A total of", "significant genes and pathways, quantitative real-time PCR (qPCR) and Western blot were performed. A to", ": gene-specific primers used in quantitative real-time PCR.Click here for additional data file. Supplem"], "order_basis": "paper_text_order:831", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["hways, quantitative real-time PCR (qPCR) and Western blot were performed. A total of 236 DEGs were cap", "f STAT3 and SOCS3 in a mouse model with DCM. Western blot results showed that the protein level of SOC"], "order_basis": "paper_text_order:856", "id": "assay:2"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ed the protein level of STAT3 and SOCS3 in a mouse model with DCM. Western blot results showed that t", "phosphorylated-STAT3 (P-STAT3) was activated in mice with DCM. In vitro results also uncovered th", "ed the protein level of STAT3 and SOCS3 in a mouse model with DCM. Western blot results showed", "a). 2.8. Cell Culture and Treatment Neonatal rat cardiomyocytes and neonatal rat cardiac fibr"], "order_basis": "paper_text_order:1449", "id": "assay:3"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["hypertrophy was evaluated by anti-α-actinin immunofluorescence staining while the phenotypic change of card", "diac fibroblasts was evaluated by anti-α-SMA immunofluorescence staining. For cell transfection, replication"], "order_basis": "paper_text_order:2812", "id": "assay:4"}, {"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": ["-α-SMA immunofluorescence staining. For cell transfection, replication-defective adenoviral vectors we"], "order_basis": "paper_text_order:2956", "id": "assay:5"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The obtained data were presented as mean ± SD (standard deviation) and assessed by the two-tailed Student's t-test."], "order_basis": "consumes_earlier_output", "id": "assay:6"}]},"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":"2026-11-04T01:44:07+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}}}