{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37700362", "kind": "science-record", "revision": 4, "content_hash": "sha256:dbf17e32bb450cce00bac77e26ff9413aa10b7908496c30b0c9ac767e470ade5", "created_at": "2026-11-01T19:02:31Z", "updated_at": "2026-11-01T22:10:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of core genes for type 2 diabetes mellitus by integrated analysis of single-cell and bulk RNA-sequencing.", "doi": "10.1186/s40001-023-01321-1", "pmid": "37700362", "authors": ["Tingting Yang", "Chaoying Yan", "Lan Yang", "Jialu Tan", "Shiqiu Jiang", "Juan Hu", "Wei Gao", "Qiang Wang", "Yansong Li"], "journal": "European journal of medical research", "year": 2023, "abstract": "BACKGROUND: The exact mechanisms of type 2 diabetes mellitus (T2DM) remain largely unknown. We intended to authenticate critical genes linked to T2DM progression by tandem single-cell sequencing and general transcriptome sequencing data.\nMETHODS: T2DM single-cell RNA-sequencing data were submitted by the Gene Expression Omnibus (GEO) database and ArrayExpress (EBI), from which gene expression matrices were retrieved. The common cell clusters and representative marker genes were ascertained by principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), CellMarker, and FindMarkers in two datasets (GSE86469 and GSE81608). T2DM-related differentially expressed marker genes were defined by intersection analysis of marker genes and GSE86468-differentially expressed genes. Receiver operating characteristic (ROC) curves were utilized to assign representative marker genes with diagnostic values by GSE86468, GSE29226 and external validation GSE29221, and their prospective target compounds were forecasted by PubChem. Besides, the R package clusterProfiler-based functional annotation was designed to unveil the intrinsic mechanisms of the target genes. At last, western blot was used to validate the alternation of CDKN1C and DLK1 expression in primary pancreatic islet cells cultured with or without 30mM glucose.\nRESULTS: Three common cell clusters were authenticated in two independent T2DM single-cell sequencing data, covering neurons, epithelial cells, and smooth muscle cells. Functional ensemble analysis disclosed an intimate association of these cell clusters with peptide/insulin secretion and pancreatic development. Pseudo-temporal trajectory analysis indicated that almost all epithelial and smooth muscle cells were of neuron origin. We characterized CDKN1C and DLK1, which were notably upregulated in T2DM samples, with satisfactory availability in recognizing three representative marker genes in non-diabetic and T2DM samples, and they were also robustly interlinked with the clinical characteristics of patients. Western blot also demonstrated that, compared with control group, the expression of CDKN1C and DLK1 were increased in primary pancreatic islet cells cultured with 30 mM glucose for 48 h. Additionally, PubChem projected 11 and 21 potential compounds for CDKN1C and DLK1, respectively.\nCONCLUSION: It is desirable that the emergence of the 2 critical genes indicated (CDKN1C and DLK1) could be catalysts for the investigation of the mechanisms of T2DM progression and the exploitation of innovative therapies.", "claims": [{"id": "claim-method", "statement": "Briefly, the expression profiles of the T2DM-related DEMGs in the GSE86468 and GSE29226 datasets were matched, the ROC curves of the corresponding genes were plotted and the AUCs were calculated by R package pROC in both datasets [57].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37700362", "locator": "sections[24] \"ROC curve-based assessment of diagnostic benefit\" paragraph 2", "quote": "Briefly, the expression profiles of the T2DM-related DEMGs in the GSE86468 and GSE29226 datasets were matched, the ROC curves of the corresponding genes were plotted and the AUCs were calculated by R package pROC in both datasets [57]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets [GSE86469, GSE81608, GSE86468, GSE29226 and GSE29221] for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress (EBI) (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/). The related code for present study could be found on GitHub at https://github.com/liyansong1987/code-for-manuscript.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37700362", "locator": "sections[33] \"Availability of data and materials\" paragraph 2", "quote": "The datasets [GSE86469, GSE81608, GSE86468, GSE29226 and GSE29221] for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress (EBI) (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/). The related code for present study could be found on GitHub at https://github.com/liyansong1987/code-for-manuscript."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The results revealed that CDKN1C and DLK1 had favorable sample discrimination in both datasets (both AUC > 0.75; Fig. 6A) and considered as critical genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37700362", "locator": "sections[9] \"Assessment of the diagnostic value and clinical relevance of the T2DM-related DEMGs\" paragraph 2", "quote": "The results revealed that CDKN1C and DLK1 had favorable sample discrimination in both datasets (both AUC > 0.75; Fig. 6A) and considered as critical genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The results revealed that CDKN1C and DLK1 had favorable sample discrimination in both datasets (both AUC > 0.75; Fig. 6A) and considered as critical genes.", "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:37700362"], "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. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:E-MTAB-5061"], "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:group_comparison_wilcoxon", "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:E-MTAB-5061"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37700362", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40001-023-01321-1", "sha256": "sha256:7c40348ef5e49e83a95f9d519f11a9b8768552c29d8faf9fd101aa6ecd44524f", "bytes": 68528, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40001-023-01321-1", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10498638", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:E-MTAB-5061", "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=E-MTAB-5061", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "E-MTAB-5061", "version": null, "note": "The datasets [GSE86469, GSE81608, GSE86468, GSE29226 and GSE29221] for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress (EBI) (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/). The related code for present study could be found on GitHub at https://github.com/liyansong1987/code-for-manuscript.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets [GSE86469, GSE81608, GSE86468, GSE29226 and GSE29221] for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress (EBI) (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/). The related code for present study could be found on GitHub at https://github.com/liyansong1987/code-for-manuscript.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": null, "resolution_checked_at": "2026-11-01T18:46:41Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE29221", "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=GSE29221", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29221", "version": null, "note": "The datasets [GSE86469, GSE81608, GSE86468, GSE29226 and GSE29221] for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress (EBI) (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/). The related code for present study could be found on GitHub at https://github.com/liyansong1987/code-for-manuscript.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets [GSE86469, GSE81608, GSE86468, GSE29226 and GSE29221] for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress (EBI) (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/). The related code for present study could be found on GitHub at https://github.com/liyansong1987/code-for-manuscript.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM722668", "GSM722669", "GSM722670", "GSM722671", "GSM722672", "GSM722673", "GSM722674", "GSM722675", "GSM722676", "GSM722677", "GSM722678", "GSM722679", "GSM722680", "GSM722681", "GSM722682", "GSM722683", "GSM722684", "GSM722685", "GSM722686", "GSM722687", "GSM722688", "GSM722689", "GSM722690", "GSM722691"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Global Gene Expression Profiles of  Skeletal Muscle in Males with Type 2 Diabetes.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE29226", "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=GSE29226", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE29226", "version": null, "note": "The datasets [GSE86469, GSE81608, GSE86468, GSE29226 and GSE29221] for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress (EBI) (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/). 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The related code for present study could be found on GitHub at https://github.com/liyansong1987/code-for-manuscript.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM722735", "GSM722736", "GSM722737", "GSM722738", "GSM722739", "GSM722740", "GSM722741", "GSM722742", "GSM722743", "GSM722744", "GSM722745", "GSM722746", "GSM722747", "GSM722748", "GSM722749", "GSM722750", "GSM722751", "GSM722752", "GSM722753", "GSM722754", "GSM722755", "GSM722756", "GSM722757", "GSM722758"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Global Gene Expression Profiles of Subcutaneous Adipose in Females with Type 2 Diabetes.", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE81608", "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=GSE81608", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE81608", "version": null, "note": "The datasets [GSE86469, GSE81608, GSE86468, GSE29226 and GSE29221] for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress (EBI) (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/). 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"GSM2158240", "GSM2158241", "GSM2158242", "GSM2158243", "GSM2158244", "GSM2158245", "GSM2158246", "GSM2158247", "GSM2158248", "GSM2158249", "GSM2158250", "GSM2158251", "GSM2158252", "GSM2158253", "GSM2158254", "GSM2158255", "GSM2158256", "GSM2158257", "GSM2158258", "GSM2158259", "GSM2158260", "GSM2158261", "GSM2158262", "GSM2158263", "GSM2158264", "GSM2158265", "GSM2158266", "GSM2158267", "GSM2158268", "GSM2158269", "GSM2158270", "GSM2158271", "GSM2158272", "GSM2158273", "GSM2158274", "GSM2158275", "GSM2158276", "GSM2158277", "GSM2158278", "GSM2158279", "GSM2158280", "GSM2158281", "GSM2158282", "GSM2158283", "GSM2158284", "GSM2158285", "GSM2158286", "GSM2158287", "GSM2158288", "GSM2158289", "GSM2158290", "GSM2158291", "GSM2158292", "GSM2158293", "GSM2158294", "GSM2158295", "GSM2158296", "GSM2158297", "GSM2158298", "GSM2158299", "GSM2158300", "GSM2158301", "GSM2158302", "GSM2158303", "GSM2158304", "GSM2158305", "GSM2158306", "GSM2158307", "GSM2158308", "GSM2158309", "GSM2158310", "GSM2158311", "GSM2158312", "GSM2158313", "GSM2158314", "GSM2158315", "GSM2158316", "GSM2158317", "GSM2158318", "GSM2158319", "GSM2158320", "GSM2158321", "GSM2158322", "GSM2158323", "GSM2158324", "GSM2158325", "GSM2158326", "GSM2158327", "GSM2158328", "GSM2158329", "GSM2158330", "GSM2158331", "GSM2158332", "GSM2158333", "GSM2158334", "GSM2158335", "GSM2158336", "GSM2158337", "GSM2158338", "GSM2158339", "GSM2158340", "GSM2158341", "GSM2158342", "GSM2158343", "GSM2158344", "GSM2158345", "GSM2158346", "GSM2158347", "GSM2158348", "GSM2158349", "GSM2158350", "GSM2158351", "GSM2158352", "GSM2158353", "GSM2158354", "GSM2158355", "GSM2158356", "GSM2158357", "GSM2158358", "GSM2158359", "GSM2158360", "GSM2158361", "GSM2158362", "GSM2158363", "GSM2158364", "GSM2158365", "GSM2158366", "GSM2158367", "GSM2158368", "GSM2158369", "GSM2158370", "GSM2158371", "GSM2158372", "GSM2158373", "GSM2158374", "GSM2158375", "GSM2158376", "GSM2158377", "GSM2158378", "GSM2158379", "GSM2158380", "GSM2158381", "GSM2158382", "GSM2158383", "GSM2158384", "GSM2158385", "GSM2158386", "GSM2158387", "GSM2158388", "GSM2158389", "GSM2158390", "GSM2158391", "GSM2158392", "GSM2158393", "GSM2158394", "GSM2158395", "GSM2158396", "GSM2158397", "GSM2158398", "GSM2158399", "GSM2158400", "GSM2158401", "GSM2158402", "GSM2158403", "GSM2158404", "GSM2158405", "GSM2158406", "GSM2158407", "GSM2158408", "GSM2158409", "GSM2158410", "GSM2158411", "GSM2158412", "GSM2158413", "GSM2158414", "GSM2158415", "GSM2158416", "GSM2158417", "GSM2158418", "GSM2158419", "GSM2158420", "GSM2158421", "GSM2158422", "GSM2158423", "GSM2158424", "GSM2158425", "GSM2158426", "GSM2158427", "GSM2158428", "GSM2158429", "GSM2158430", "GSM2158431", "GSM2158432", "GSM2158433", "GSM2158434", "GSM2158435", "GSM2158436", "GSM2158437", "GSM2158438", "GSM2158439", "GSM2158440", "GSM2158441", "GSM2158442", "GSM2158443", "GSM2158444", "GSM2158445", "GSM2158446", "GSM2158447", "GSM2158448", "GSM2158449", "GSM2158450", "GSM2158451", "GSM2158452", "GSM2158453", "GSM2158454", "GSM2158455", "GSM2158456", "GSM2158457", "GSM2158458", "GSM2158459", "GSM2158460", "GSM2158461", "GSM2158462", "GSM2158463", "GSM2158464", "GSM2158465", "GSM2158466", "GSM2158467", "GSM2158468", "GSM2158469", "GSM2158470", "GSM2158471", "GSM2158472", "GSM2158473", "GSM2158474", "GSM2158475", "GSM2158476", "GSM2158477", "GSM2158478", "GSM2158479", "GSM2158480", "GSM2158481", "GSM2158482", "GSM2158483", "GSM2158484", "GSM2158485", "GSM2158486", "GSM2158487", "GSM2158488", "GSM2158489", "GSM2158490", "GSM2158491", "GSM2158492", "GSM2158493", "GSM2158494", "GSM2158495", "GSM2158496", "GSM2158497", "GSM2158498", "GSM2158499", "GSM2158500", "GSM2158501", "GSM2158502", "GSM2158503", "GSM2158504", "GSM2158505", "GSM2158506", "GSM2158507", "GSM2158508", "GSM2158509", "GSM2158510", "GSM2158511", "GSM2158512", "GSM2158513", "GSM2158514", "GSM2158515", "GSM2158516", "GSM2158517", "GSM2158518", "GSM2158519", "GSM2158520", "GSM2158521", "GSM2158522", "GSM2158523", "GSM2158524", "GSM2158525", "GSM2158526", "GSM2158527", "GSM2158528", "GSM2158529", "GSM2158530", "GSM2158531", "GSM2158532", "GSM2158533", "GSM2158534", "GSM2158535", "GSM2158536", "GSM2158537", "GSM2158538", "GSM2158539", "GSM2158540", "GSM2158541", "GSM2158542", "GSM2158543", "GSM2158544", "GSM2158545", "GSM2158546", "GSM2158547", "GSM2158548", "GSM2158549", "GSM2158550", "GSM2158551", "GSM2158552", "GSM2158553", "GSM2158554", "GSM2158555", "GSM2158556", "GSM2158557", "GSM2158558", "GSM2158559", "GSM2158560", "GSM2158561", "GSM2158562", "GSM2158563", "GSM2158564", "GSM2158565", "GSM2158566", "GSM2158567", "GSM2158568", "GSM2158569", "GSM2158570", "GSM2158571", "GSM2158572", "GSM2158573", "GSM2158574", "GSM2158575", "GSM2158576", "GSM2158577", "GSM2158578", "GSM2158579", "GSM2158580", "GSM2158581", "GSM2158582", "GSM2158583", "GSM2158584", "GSM2158585", "GSM2158586", "GSM2158587", "GSM2158588", "GSM2158589", "GSM2158590", "GSM2158591", "GSM2158592", "GSM2158593", "GSM2158594", "GSM2158595", "GSM2158596", "GSM2158597", "GSM2158598", "GSM2158599", "GSM2158600", "GSM2158601", "GSM2158602", "GSM2158603", "GSM2158604", "GSM2158605", "GSM2158606", "GSM2158607", "GSM2158608", "GSM2158609", "GSM2158610", "GSM2158611", "GSM2158612", "GSM2158613", "GSM2158614", "GSM2158615", "GSM2158616", "GSM2158617", "GSM2158618", "GSM2158619", "GSM2158620", "GSM2158621", "GSM2158622", "GSM2158623", "GSM2158624", "GSM2158625", "GSM2158626", "GSM2158627", "GSM2158628", "GSM2158629", "GSM2158630", "GSM2158631", "GSM2158632", "GSM2158633", "GSM2158634", "GSM2158635", "GSM2158636", "GSM2158637", "GSM2158638", "GSM2158639", "GSM2158640", "GSM2158641", "GSM2158642", "GSM2158643", "GSM2158644", "GSM2158645", "GSM2158646", "GSM2158647", "GSM2158648", "GSM2158649", "GSM2158650", "GSM2158651", "GSM2158652", "GSM2158653", "GSM2158654", "GSM2158655", "GSM2158656", "GSM2158657", "GSM2158658", "GSM2158659", "GSM2158660", "GSM2158661", "GSM2158662", "GSM2158663", "GSM2158664", "GSM2158665", "GSM2158666", "GSM2158667", "GSM2158668", "GSM2158669", "GSM2158670", "GSM2158671", "GSM2158672", "GSM2158673", "GSM2158674", "GSM2158675", "GSM2158676", "GSM2158677", "GSM2158678", "GSM2158679", "GSM2158680", "GSM2158681", "GSM2158682", "GSM2158683", "GSM2158684", "GSM2158685", "GSM2158686", "GSM2158687", "GSM2158688", "GSM2158689", "GSM2158690", "GSM2158691", "GSM2158692", "GSM2158693", "GSM2158694", "GSM2158695", "GSM2158696", "GSM2158697", "GSM2158698", "GSM2158699", "GSM2158700", "GSM2158701", "GSM2158702", "GSM2158703", "GSM2158704", "GSM2158705", "GSM2158706", "GSM2158707", "GSM2158708", "GSM2158709", "GSM2158710", "GSM2158711", "GSM2158712", "GSM2158713", "GSM2158714", "GSM2158715", "GSM2158716", "GSM2158717", "GSM2158718", "GSM2158719", "GSM2158720", "GSM2158721", "GSM2158722", "GSM2158723", "GSM2158724", "GSM2158725", "GSM2158726", "GSM2158727", "GSM2158728", "GSM2158729", "GSM2158730", "GSM2158731", "GSM2158732", "GSM2158733", "GSM2158734", "GSM2158735", "GSM2158736", "GSM2158737", "GSM2158738", "GSM2158739", "GSM2158740", "GSM2158741", "GSM2158742", "GSM2158743", "GSM2158744", "GSM2158745", "GSM2158746", "GSM2158747", "GSM2158748", "GSM2158749", "GSM2158750", "GSM2158751", "GSM2158752", "GSM2158753", "GSM2158754", "GSM2158755", "GSM2158756", "GSM2158757", "GSM2158758", "GSM2158759", "GSM2158760", "GSM2158761", "GSM2158762", "GSM2158763", "GSM2158764", "GSM2158765", "GSM2158766", "GSM2158767", "GSM2158768", "GSM2158769", "GSM2158770", "GSM2158771", "GSM2158772", "GSM2158773", "GSM2158774", "GSM2158775", "GSM2158776", "GSM2158777", "GSM2158778", "GSM2158779", "GSM2158780", "GSM2158781", "GSM2158782", "GSM2158783", "GSM2158784", "GSM2158785", "GSM2158786", "GSM2158787", "GSM2158788", "GSM2158789", "GSM2158790", "GSM2158791", "GSM2158792", "GSM2158793", "GSM2158794", "GSM2158795", "GSM2158796", "GSM2158797", "GSM2158798", "GSM2158799", "GSM2158800", "GSM2158801", "GSM2158802", "GSM2158803", "GSM2158804", "GSM2158805", "GSM2158806", "GSM2158807", "GSM2158808", "GSM2158809", "GSM2158810", "GSM2158811", "GSM2158812", "GSM2158813", "GSM2158814", "GSM2158815", "GSM2158816", "GSM2158817", "GSM2158818", "GSM2158819", "GSM2158820", "GSM2158821", "GSM2158822", "GSM2158823", "GSM2158824", "GSM2158825", "GSM2158826", "GSM2158827", "GSM2158828", "GSM2158829", "GSM2158830", "GSM2158831", "GSM2158832", "GSM2158833", "GSM2158834", "GSM2158835", "GSM2158836", "GSM2158837", "GSM2158838", "GSM2158839", "GSM2158840", "GSM2158842", "GSM2158843", "GSM2158844", "GSM2158846", "GSM2158848", "GSM2158849", "GSM2158850", "GSM2158852", "GSM2158853", "GSM2158855", "GSM2158856", "GSM2158858", "GSM2158859", "GSM2158861", "GSM2158862", "GSM2158863", "GSM2158865", "GSM2158866", "GSM2158868", "GSM2158869", "GSM2158871", "GSM2158872", "GSM2158874", "GSM2158875", "GSM2158877", "GSM2158878", "GSM2158879", "GSM2158881", "GSM2158882", "GSM2158884", "GSM2158885", "GSM2158887", "GSM2158888", "GSM2158889", "GSM2158891", "GSM2158892", "GSM2158894", "GSM2158895", "GSM2158896", "GSM2158898", "GSM2158899", "GSM2158901", "GSM2158902", "GSM2158904", "GSM2158906", "GSM2158907", "GSM2158908", "GSM2158910", "GSM2158911", "GSM2158913", "GSM2158914", "GSM2158916", "GSM2158917", "GSM2158919", "GSM2158920", "GSM2158922", "GSM2158923", "GSM2158925", "GSM2158926", "GSM2158928", "GSM2158929", "GSM2158931", "GSM2158932", "GSM2158934", "GSM2158935", "GSM2158936", "GSM2158937", "GSM2158938", "GSM2158939", "GSM2158940", "GSM2158941", "GSM2158942", "GSM2158943", "GSM2158944", "GSM2158945", "GSM2158946", "GSM2158947", "GSM2158948", "GSM2158949", "GSM2158950", "GSM2158951", "GSM2158952", "GSM2158953", "GSM2158954", "GSM2158955", "GSM2158956", "GSM2158957", "GSM2158958", "GSM2158959", "GSM2158960", "GSM2158961", "GSM2158962", "GSM2158963", "GSM2158964", "GSM2158965", "GSM2158966", "GSM2158967", "GSM2158968", "GSM2158969", "GSM2158970", "GSM2158971", "GSM2158972", "GSM2158973", "GSM2158974", "GSM2158975", "GSM2158976", "GSM2158977", "GSM2158978", "GSM2158979", "GSM2158980", "GSM2158981", "GSM2158982", "GSM2158983", "GSM2158984", "GSM2158985", "GSM2158986", "GSM2158987", "GSM2158988", "GSM2158989", "GSM2158990", "GSM2158991", "GSM2158992", "GSM2158993", "GSM2158994", "GSM2158995", "GSM2158996", "GSM2158997", "GSM2158998", "GSM2158999", "GSM2159000", "GSM2159001", "GSM2159002", "GSM2159003", "GSM2159004", "GSM2159005", "GSM2159006", "GSM2159007", "GSM2159008", "GSM2159009", "GSM2159010", "GSM2159011", "GSM2159012", "GSM2159013", "GSM2159014", "GSM2159015", "GSM2159016", "GSM2159017", "GSM2159018", "GSM2159019", "GSM2159020", "GSM2159021", "GSM2159022", "GSM2159023", "GSM2159024", "GSM2159025", "GSM2159026", "GSM2159027", "GSM2159028", "GSM2159029", "GSM2159030", "GSM2159031", "GSM2159032", "GSM2159033", "GSM2159034", "GSM2159035", "GSM2159036", "GSM2159037", "GSM2159038", "GSM2159039", "GSM2159040", "GSM2159041", "GSM2159042", "GSM2159043", "GSM2159044", "GSM2159045", "GSM2159046", "GSM2159047", "GSM2159048", "GSM2159049", "GSM2159050", "GSM2159051", "GSM2159052", "GSM2159053", "GSM2159054", "GSM2159055", "GSM2159056", "GSM2159057", "GSM2159058", "GSM2159059", "GSM2159060", "GSM2159061", "GSM2159062", "GSM2159063", "GSM2159064", "GSM2159065", "GSM2159066", "GSM2159067", "GSM2159068", "GSM2159069", "GSM2159070", "GSM2159071", "GSM2159072", "GSM2159073", "GSM2159074", "GSM2159075", "GSM2159076", "GSM2159077", "GSM2159078", "GSM2159079", "GSM2159080", "GSM2159081", "GSM2159082", "GSM2159083", "GSM2159084", "GSM2159085", "GSM2159086", "GSM2159087", "GSM2159088", "GSM2159089", "GSM2159090", "GSM2159091", "GSM2159092", "GSM2159093", "GSM2159094", "GSM2159095", "GSM2159096", "GSM2159097", "GSM2159098", "GSM2159099", "GSM2159100", "GSM2159101", "GSM2159102", "GSM2159103", "GSM2159104", "GSM2159105", "GSM2159106", "GSM2159107", "GSM2159108", "GSM2159109", "GSM2159110", "GSM2159111", "GSM2159112", "GSM2159113", "GSM2159114", "GSM2159115", "GSM2159116", "GSM2159117", "GSM2159118", "GSM2159119", "GSM2159120", "GSM2159121", "GSM2159122", "GSM2159123", "GSM2159124", "GSM2159125", "GSM2159126", "GSM2159127", "GSM2159128", "GSM2159129", "GSM2159130", "GSM2159131", "GSM2159132", "GSM2159133", "GSM2159134", "GSM2159135", "GSM2159136", "GSM2159137", "GSM2159138", "GSM2159139", "GSM2159140", "GSM2159141", "GSM2159142", "GSM2159143", "GSM2159144", "GSM2159145", "GSM2159146", "GSM2159147", "GSM2159148", "GSM2159149", "GSM2159150", "GSM2159151", "GSM2159152", "GSM2159153", "GSM2159154", "GSM2159155", "GSM2159156", "GSM2159157", "GSM2159158", "GSM2159159", "GSM2159160", "GSM2159161", "GSM2159162", "GSM2159163", "GSM2159164", "GSM2159165", "GSM2159166", "GSM2159167", "GSM2159168", "GSM2159169", "GSM2159170", "GSM2159171", "GSM2159172", "GSM2159173", "GSM2159174", "GSM2159175", "GSM2159176", "GSM2159177", "GSM2159178", "GSM2159179", "GSM2159180", "GSM2159181", "GSM2159182", "GSM2159183", "GSM2159184", "GSM2159185", "GSM2159186", "GSM2159187", "GSM2159188", "GSM2159189", "GSM2159190", "GSM2159191", "GSM2159192", "GSM2159193", "GSM2159194", "GSM2159195", "GSM2159196", "GSM2159197", "GSM2159198", "GSM2159199", "GSM2159200", "GSM2159201", "GSM2159202", "GSM2159203", "GSM2159204", "GSM2159205", "GSM2159206", "GSM2159207", "GSM2159208", "GSM2159209", "GSM2159210", "GSM2159211", "GSM2159212", "GSM2159213", "GSM2159214", "GSM2159215", "GSM2159216", "GSM2159217", "GSM2159218", "GSM2159219", "GSM2159220", "GSM2159221", "GSM2159222", "GSM2159223", "GSM2159224", "GSM2159225", "GSM2159226", "GSM2159227", "GSM2159228", "GSM2159229", "GSM2159230", "GSM2159231", "GSM2159235", "GSM2159238", "GSM2159240", "GSM2159243", "GSM2159245", "GSM2159248", "GSM2159251", "GSM2159254", "GSM2159256", "GSM2159258", "GSM2159261", "GSM2159263", "GSM2159266", "GSM2159269", "GSM2159271", "GSM2159274", "GSM2159277", "GSM2159279", "GSM2159280", "GSM2159281", "GSM2159282", "GSM2159283", "GSM2159284", "GSM2159285", "GSM2159286", "GSM2159287", "GSM2159288", "GSM2159289", "GSM2159290", "GSM2159291", "GSM2159292", "GSM2159293", "GSM2159294", "GSM2159295", "GSM2159296", "GSM2159297", "GSM2159298", "GSM2159299", "GSM2159300", "GSM2159301", "GSM2159302", "GSM2159303", "GSM2159304", "GSM2159305", "GSM2159306", "GSM2159307", "GSM2159308", "GSM2159309", "GSM2159310", "GSM2159311", "GSM2159312", "GSM2159313", "GSM2159314", "GSM2159315", "GSM2159316", "GSM2159317", "GSM2159318", "GSM2159319", "GSM2159320", "GSM2159321", "GSM2159322", "GSM2159323", "GSM2159324", "GSM2159325", "GSM2159326", "GSM2159327", "GSM2159328", "GSM2159329", "GSM2159330", "GSM2159331", "GSM2159332", "GSM2159333", "GSM2159334", "GSM2159335", "GSM2159336", "GSM2159337", "GSM2159338", "GSM2159339", "GSM2159340", "GSM2159341", "GSM2159342", "GSM2159343", "GSM2159344", "GSM2159345", "GSM2159346", "GSM2159347", "GSM2159348", "GSM2159349", "GSM2159350", "GSM2159351", "GSM2159352", "GSM2159353", "GSM2159354", "GSM2159355", "GSM2159356", "GSM2159357", "GSM2159358", "GSM2159359", "GSM2159360", "GSM2159361", "GSM2159362", "GSM2159363", "GSM2159364", "GSM2159365", "GSM2159366", "GSM2159367", "GSM2159368", "GSM2159369", "GSM2159370", "GSM2159371", "GSM2159372", "GSM2159373", "GSM2159374", "GSM2159375", "GSM2159376", "GSM2159377", "GSM2159378", "GSM2159379", "GSM2159380", "GSM2159381", "GSM2159382", "GSM2159383", "GSM2159384", "GSM2159385", "GSM2159386", "GSM2159387", "GSM2159388", "GSM2159389", "GSM2159390", "GSM2159391", "GSM2159392", "GSM2159393", "GSM2159394", "GSM2159395", "GSM2159396", "GSM2159397", "GSM2159398", "GSM2159399", "GSM2159400", "GSM2159401", "GSM2159402", "GSM2159403", "GSM2159404", "GSM2159405", "GSM2159406", "GSM2159407", "GSM2159408", "GSM2159409", "GSM2159410", "GSM2159411", "GSM2159412", "GSM2159413", "GSM2159414", "GSM2159415", "GSM2159416", "GSM2159417", "GSM2159418", "GSM2159419", "GSM2159420", "GSM2159421", "GSM2159422", "GSM2159423", "GSM2159424", "GSM2159425", "GSM2159426", "GSM2159427", "GSM2159428", "GSM2159429", "GSM2159430", "GSM2159431", "GSM2159432", "GSM2159433", "GSM2159434", "GSM2159435", 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"asset:data:geo:GSE86468 not downloaded", "asset:data:geo:GSE86468 licence not read", "asset:data:geo:GSE86469 not downloaded", "asset:data:geo:GSE86469 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "principal component analysis"}}, {"id": "method-3", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {"fold_change": "kage limma, using |log2 FC|> 0", "log2fc_threshold": "R package limma, using |log2 FC|> 0"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-4", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-5", "family": "clustering", "specific": "kmeans", "label": "Clustering", "dsl_operations": ["kmeans_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "K-means"}}, {"id": "method-6", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "dendrogram"}}, {"id": "method-7", "family": "image_quantification", "specific": "densitometry", "label": "Image analysis / quantification", "dsl_operations": ["segment_objects", "quantify_intensity"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["image_stack"], "evidence": {"score": 0.8, "band": "high", "quote": "Densitometr"}}, {"id": "method-8", "family": null, "specific": null, "label": "receiver operating characteristic (ROC) curve analysis using R package pROC", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Briefly, the expression profiles of the T2DM-related DEMGs in the GSE86468 and GSE29226 datasets were matched, the ROC curves of the corresponding genes were plotted and the AUCs were calculated by R package pROC in both datasets [57]."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE86469", "GSE81608", "E-MTAB-5061", "GSE86468", "GSE29226", "GSE29221"], "resolved_accessions": ["GSE86469", "GSE81608", "E-MTAB-5061", "GSE86468", "GSE29226", "GSE29221"], "statements": ["The datasets [GSE86469, GSE81608, GSE86468, GSE29226 and GSE29221] for this study can be found in the GEO database (https://www.ncbi.nlm.nih.gov/geo/) and ArrayExpress (EBI) (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/). The related code for present study could be found on GitHub at https://github.com/liyansong1987/code-for-manuscript."], "basis": "The paper names GSE86469, GSE81608, E-MTAB-5061, GSE86468, GSE29226, GSE29221 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:37700362", "data:geo:E-MTAB-5061"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:E-MTAB-5061"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:53:18Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 19972, "completion_tokens": 2933, "cached_tokens": 128}}, "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:37700362", "type": "paper", "label": "pmid:37700362"}, {"id": "source:pmid:37700362", "type": "manuscript", "label": "PMID 37700362 full text"}, {"id": "data:geo:E-MTAB-5061", "type": "dataset", "label": "GEO E-MTAB-5061"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37700362", "type": "paper", "label": "pmid:37700362"}, {"id": "source:pmid:37700362", "type": "manuscript", "label": "PMID 37700362 full text"}, {"id": "data:geo:E-MTAB-5061", "type": "dataset", "label": "GEO E-MTAB-5061"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37700362", "type": "extraction", "used": ["source:pmid:37700362"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-E-MTAB-5061", "type": "accession_resolution", "used": ["data:geo:E-MTAB-5061"], "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:37700362", "parent_hash": "sha256:75d1798ba5b9aa5a021b3db01ac597ae95e4bcb8e07d94db1d8b91a062af24a0", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:E-MTAB-5061 licence not read", "asset:data:geo:E-MTAB-5061 not downloaded", "asset:data:geo:GSE29221 licence not read", "asset:data:geo:GSE29221 not downloaded", "asset:data:geo:GSE29226 licence not read", "asset:data:geo:GSE29226 not downloaded", "asset:data:geo:GSE81608 licence not read", "asset:data:geo:GSE81608 not downloaded", "asset:data:geo:GSE86468 licence not read", "asset:data:geo:GSE86468 not downloaded", "asset:data:geo:GSE86469 licence not read", "asset:data:geo:GSE86469 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["integrated analysis of single-cell and bulk RNA-sequencing.", "e sequencing data. METHODS: T2DM single-cell RNA-sequencing data were submitted by the Gene Expression O", "nalysis of T2DM-related DEMGs combining bulk RNA-seq and single cell data. A The volcano plot of", "ed DEGs by cross-tabulation analysis of bulk RNA-seq and single cell data. C GO analysis of T2DM-"], "order_basis": "paper_text_order:76", "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": ["sic mechanisms of the target genes. At last, western blot was used to validate the alternation of CDKN", "th the clinical characteristics of patients. Western blot also demonstrated that, compared with contro", "). Expression analysis of CDKN1C and DLK1 by western blotting The expression of CDKN1C and DLK1 was furthe", "under different conditions. A Representative western blot of CDKN1C and DLK1 in primary pancreatic isl"], "order_basis": "paper_text_order:1287", "id": "assay:2"}, {"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": ["expression in primary pancreatic islet cells cultured with or without 30mM glucose. RESULTS: Three comm", "increased in primary pancreatic islet cells cultured with 30 mM glucose for 48 h. Additionally, PubChe"], "order_basis": "paper_text_order:1401", "id": "assay:3"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.642, "evidence": ["of CDKN1C and DLK1 was further confirmed in rat pancreatic islet cells. Compared with contro"], "order_basis": "paper_text_order:7048", "id": "assay:4"}, {"role": "data_generation", "definition_id": "clinical_trial", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["C and DLK1 in primary pancreatic islet cells treated with or without 30 mM glucose (HG) for 48 h. B Densitometric"], "order_basis": "paper_text_order:7377", "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": 0.8, "evidence": ["Wilcoxon"], "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":"2026-11-04T02:35:38+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}}}