{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36914941", "kind": "science-record", "revision": 3, "content_hash": "sha256:a43872e4d5a58a1263982679c0b10848036a6314f8f5e2e606dbd7ab220ab44c", "created_at": "2026-11-01T19:01:33Z", "updated_at": "2026-11-01T22:09:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-cell profiling of the copy-number heterogeneity in colorectal cancer.", "doi": "10.1097/CM9.0000000000002469", "pmid": "36914941", "authors": ["Shiyu Song", "Lin Feng", "Kexing Xi", "Zhigang Sun", "Deyang Kong", "Zhenkai Luo", "Wei Pei", "Haizeng Zhang"], "journal": "Chinese medical journal", "year": 2023, "abstract": "BACKGROUND: With functionally heterogeneous cells, tumors comprise a complex ecosystem to promote tumor adaptability and evolution under strong selective pressure from the given microenvironment. Diversifying tumor cells or intra-tumor heterogeneity is essential for tumor growth, invasion, and immune evasion. However, no reliable method to classify tumor cell subtypes is yet available. In this study, we introduced the single-cell sequencing combined with copy number characteristics to identify the types of tumor cells in microsatellite stable (MSS) colorectal cancer (CRC).\nMETHODS: To characterize the somatic copy number alteration (SCNA) of MSS CRC in a single cell profile, we analyzed 26 tissue samples from 19 Korean patients (GSE132465, the Samsung Medical Center [SMC] dataset) and then verified our findings with 15 tissue samples from five Belgian patients (GSE144735, the Katholieke Universiteit Leuven 3 [KUL3] dataset). The Cancer Genome Atlas (TCGA) cohort, GSE39582 cohort, and National Cancer Center (NCC) cohort (24 MSS CRC patients were enrolled in this study between March 2017 and October 2017) were used to validate the clinical features of prognostic signatures.\nRESULTS: We employed single cell RNA-sequencing data to identify three types of tumor cells in MSS CRC by their SCNA characteristics. Among these three types of tumor cells, C1 and C3 had a higher SCNA burden; C1 had significant chromosome 13 and 20 amplification, whereas C3 was the polar opposite of C1, which exhibited deletion in chromosome 13 and 20. The three types of tumor cells exhibited various functions in the tumor microenvironment and harbored different mutations. C1 and C2 were linked to the immune response and hypoxia, respectively, while C3 was critical for cell adhesion activity and tumor angiogenesis. Additionally, one gene ( OLFM4 ) was identified as epithelium-specific biomarker of better prognosis of CRC (TCGA cohort: P = 0.0110; GSE39582 cohort: P = 0.0098; NCC cohort: P = 0.0360).\nCONCLUSIONS: On the basis of copy number characteristics, we illustrated tumor heterogeneity in MSS CRC and identified three types of tumor cells with distinct roles in tumor microenvironment. By understanding heterogeneity in the intricate tumor microenvironment, we gained an insight into the mechanisms of tumor evolution, which may support the development of therapeutic strategies.", "claims": [{"id": "claim-method", "statement": "On the basis of log-rank testing, Kaplan–Meier curves were used to evaluate overall survival differences between different gene expression level groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36914941", "locator": "sections[13] \"Identification of the prognostic signature of chromosomes 13 and 20\" paragraph 2", "quote": "On the basis of log-rank testing, Kaplan–Meier curves were used to evaluate overall survival differences between different gene expression level groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36914941", "locator": "sections[4] \"Public data availability and preprocessing\" paragraph 2", "quote": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients)."}], "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:36914941"], "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:GSE132465"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE132465"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36914941", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/CM9.0000000000002469", "sha256": "sha256:94fb60bc730fa0cb629889c12d22a22fa9ddb4da035d5464ce8fac16fce900ba", "bytes": 54415, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/CM9.0000000000002469", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10129169", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE132465", "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=GSE132465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE132465", "version": null, "note": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3868425", "GSM3868426", "GSM3868427", "GSM3868428", "GSM3868429", "GSM3868430", "GSM3868431", "GSM3868432", "GSM3868433", "GSM3868434", "GSM3868435", "GSM3868436", "GSM3868437", "GSM3868438", "GSM3868439", "GSM3868440", "GSM3868441", "GSM3868442", "GSM3868443", "GSM3868444", "GSM3868445", "GSM3868446", "GSM3868447", "GSM3868448", "GSM3868449", "GSM3868450", "GSM3868451", "GSM3868452", "GSM3868453", "GSM3868454", "GSM3868455", "GSM3868456", "GSM3868457"], "sample_count": 33, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Single cell 3' RNA sequencing of 23 Korean colorectal cancer patients", "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:GSE144735", "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=GSE144735", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE144735", "version": null, "note": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM4294474", "GSM4294475", "GSM4294476", "GSM4294477", "GSM4294478", "GSM4294479", "GSM4294480", "GSM4294481", "GSM4294482", "GSM4294483", "GSM4294484", "GSM4294485", "GSM4294486", "GSM4294487", "GSM4294488", "GSM4294489", "GSM4294490", "GSM4294491"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "24676", "taxon": "Homo sapiens", "title": "Single cell 3' RNA sequencing of 6 Belgian colorectal cancer patients", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE39582", "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=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1681353", "GSM1681354", "GSM1681355", "GSM1681356", "GSM1681357", "GSM1681358", "GSM1681359", "GSM1681360", "GSM1681361", "GSM1681362", "GSM1681363", "GSM1681364", "GSM1681365", "GSM1681366", "GSM1681367", "GSM1681368", "GSM1681369", "GSM1681370", "GSM1681371", "GSM971957", "GSM971958", "GSM971959", "GSM971960", "GSM971961", "GSM971962", "GSM971963", "GSM971964", "GSM971965", "GSM971966", "GSM971967", "GSM971968", "GSM971969", "GSM971970", "GSM971971", "GSM971972", "GSM971973", "GSM971974", "GSM971975", "GSM971976", "GSM971977", "GSM971978", "GSM971979", "GSM971980", "GSM971981", "GSM971982", "GSM971983", "GSM971984", "GSM971985", "GSM971986", "GSM971987", "GSM971988", "GSM971989", "GSM971990", "GSM971991", "GSM971992", "GSM971993", "GSM971994", "GSM971995", "GSM971996", "GSM971997", "GSM971998", "GSM971999", "GSM972000", "GSM972001", "GSM972002", "GSM972003", "GSM972004", "GSM972005", "GSM972006", "GSM972007", "GSM972008", "GSM972009", "GSM972010", "GSM972011", "GSM972012", "GSM972013", "GSM972014", "GSM972015", "GSM972016", "GSM972017", "GSM972018", "GSM972019", "GSM972020", "GSM972021", "GSM972022", "GSM972023", "GSM972024", "GSM972025", "GSM972026", "GSM972027", "GSM972028", "GSM972029", "GSM972030", "GSM972031", "GSM972032", "GSM972033", "GSM972034", "GSM972035", "GSM972036", "GSM972037", "GSM972038", "GSM972039", "GSM972040", "GSM972041", "GSM972042", "GSM972043", "GSM972044", "GSM972045", "GSM972046", "GSM972047", "GSM972048", "GSM972049", "GSM972050", "GSM972051", "GSM972052", "GSM972053", "GSM972054", "GSM972055", "GSM972056", "GSM972057", "GSM972058", "GSM972059", "GSM972060", "GSM972061", "GSM972062", "GSM972063", "GSM972064", "GSM972065", "GSM972066", "GSM972067", "GSM972068", "GSM972069", "GSM972070", "GSM972071", "GSM972072", "GSM972073", "GSM972074", "GSM972075", "GSM972076", "GSM972077", "GSM972078", "GSM972079", "GSM972080", "GSM972081", "GSM972082", "GSM972083", "GSM972084", "GSM972085", "GSM972086", "GSM972087", "GSM972088", "GSM972089", "GSM972090", "GSM972091", "GSM972092", "GSM972093", "GSM972094", "GSM972095", "GSM972096", "GSM972097", "GSM972098", "GSM972099", "GSM972100", "GSM972101", "GSM972102", "GSM972103", "GSM972104", "GSM972105", "GSM972106", "GSM972107", "GSM972108", "GSM972109", "GSM972110", "GSM972111", "GSM972112", "GSM972113", "GSM972114", "GSM972115", "GSM972116", "GSM972117", "GSM972118", "GSM972119", "GSM972120", "GSM972121", "GSM972122", "GSM972123", "GSM972124", "GSM972125", "GSM972126", "GSM972127", "GSM972128", "GSM972129", "GSM972130", "GSM972131", "GSM972132", "GSM972133", "GSM972134", "GSM972135", "GSM972136", "GSM972137", "GSM972138", "GSM972139", "GSM972140", "GSM972141", "GSM972142", "GSM972143", "GSM972144", "GSM972145", "GSM972146", "GSM972147", "GSM972148", "GSM972149", "GSM972150", "GSM972151", "GSM972152", "GSM972153", "GSM972154", "GSM972155", "GSM972156", "GSM972157", "GSM972158", "GSM972159", "GSM972160", "GSM972161", "GSM972162", "GSM972163", "GSM972164", "GSM972165", "GSM972166", "GSM972167", "GSM972168", "GSM972169", "GSM972170", "GSM972171", "GSM972172", "GSM972173", "GSM972174", "GSM972175", "GSM972176", "GSM972177", "GSM972178", "GSM972179", "GSM972180", "GSM972181", "GSM972182", "GSM972183", "GSM972184", "GSM972185", "GSM972186", "GSM972187", "GSM972188", "GSM972189", "GSM972190", "GSM972191", "GSM972192", "GSM972193", "GSM972194", "GSM972195", "GSM972196", "GSM972197", "GSM972198", "GSM972199", "GSM972200", "GSM972201", "GSM972202", "GSM972203", "GSM972204", "GSM972205", "GSM972206", "GSM972207", "GSM972208", "GSM972209", "GSM972210", "GSM972211", "GSM972212", "GSM972213", "GSM972214", "GSM972215", "GSM972216", "GSM972217", "GSM972218", "GSM972219", "GSM972220", "GSM972221", "GSM972222", "GSM972223", "GSM972224", "GSM972225", "GSM972226", "GSM972227", "GSM972228", "GSM972229", "GSM972230", "GSM972231", "GSM972232", "GSM972233", "GSM972234", "GSM972235", "GSM972236", "GSM972237", "GSM972238", "GSM972239", "GSM972240", "GSM972241", "GSM972242", "GSM972243", "GSM972244", "GSM972245", "GSM972246", "GSM972247", "GSM972248", "GSM972249", "GSM972250", "GSM972251", "GSM972252", "GSM972253", "GSM972254", "GSM972255", "GSM972256", "GSM972257", "GSM972258", "GSM972259", "GSM972260", "GSM972261", "GSM972262", "GSM972263", "GSM972264", "GSM972265", "GSM972266", "GSM972267", "GSM972268", "GSM972269", "GSM972270", "GSM972271", "GSM972272", "GSM972273", "GSM972274", "GSM972275", "GSM972276", "GSM972277", "GSM972278", "GSM972279", "GSM972280", "GSM972281", "GSM972282", "GSM972283", "GSM972284", "GSM972285", "GSM972286", "GSM972287", "GSM972288", "GSM972289", "GSM972290", "GSM972291", "GSM972292", "GSM972293", "GSM972294", "GSM972295", "GSM972296", "GSM972297", "GSM972298", "GSM972299", "GSM972300", "GSM972301", "GSM972302", "GSM972303", "GSM972304", "GSM972305", "GSM972306", "GSM972307", "GSM972308", "GSM972309", "GSM972310", "GSM972311", "GSM972312", "GSM972313", "GSM972314", "GSM972315", "GSM972316", "GSM972317", "GSM972318", "GSM972319", "GSM972320", "GSM972321", "GSM972322", "GSM972323", "GSM972324", "GSM972325", "GSM972326", "GSM972327", "GSM972328", "GSM972329", "GSM972330", "GSM972331", "GSM972332", "GSM972333", "GSM972334", "GSM972335", "GSM972336", "GSM972337", "GSM972338", "GSM972339", "GSM972340", "GSM972341", "GSM972342", "GSM972343", "GSM972344", "GSM972345", "GSM972346", "GSM972347", "GSM972348", "GSM972349", "GSM972350", "GSM972351", "GSM972352", "GSM972353", "GSM972354", "GSM972355", "GSM972356", "GSM972357", "GSM972358", "GSM972359", "GSM972360", "GSM972361", "GSM972362", "GSM972363", "GSM972364", "GSM972365", "GSM972366", "GSM972367", "GSM972368", "GSM972369", "GSM972370", "GSM972371", "GSM972372", "GSM972373", "GSM972374", "GSM972375", "GSM972376", "GSM972377", "GSM972378", "GSM972379", "GSM972380", "GSM972381", "GSM972382", "GSM972383", "GSM972384", "GSM972385", "GSM972386", "GSM972387", "GSM972388", "GSM972389", "GSM972390", "GSM972391", "GSM972392", "GSM972393", "GSM972394", "GSM972395", "GSM972396", "GSM972397", "GSM972398", "GSM972399", "GSM972400", "GSM972401", "GSM972402", "GSM972403", "GSM972404", "GSM972405", "GSM972406", "GSM972407", "GSM972408", "GSM972409", "GSM972410", "GSM972411", "GSM972412", "GSM972413", "GSM972414", "GSM972415", "GSM972416", "GSM972417", "GSM972418", "GSM972419", "GSM972420", "GSM972421", "GSM972422", "GSM972423", "GSM972424", "GSM972425", "GSM972426", "GSM972427", "GSM972428", "GSM972429", "GSM972430", "GSM972431", "GSM972432", "GSM972433", "GSM972434", "GSM972435", "GSM972436", "GSM972437", "GSM972438", "GSM972439", "GSM972440", "GSM972441", "GSM972442", "GSM972443", "GSM972444", "GSM972445", "GSM972446", "GSM972447", "GSM972448", "GSM972449", "GSM972450", "GSM972451", "GSM972452", "GSM972453", "GSM972454", "GSM972455", "GSM972456", "GSM972457", "GSM972458", "GSM972459", "GSM972460", "GSM972461", "GSM972462", "GSM972463", "GSM972464", "GSM972465", "GSM972466", "GSM972467", "GSM972468", "GSM972469", "GSM972470", "GSM972471", "GSM972472", "GSM972473", "GSM972474", "GSM972475", "GSM972476", "GSM972477", "GSM972478", "GSM972479", "GSM972480", "GSM972481", "GSM972482", "GSM972483", "GSM972484", "GSM972485", "GSM972486", "GSM972487", "GSM972488", "GSM972489", "GSM972490", "GSM972491", "GSM972492", "GSM972493", "GSM972494", "GSM972495", "GSM972496", "GSM972497", "GSM972498", "GSM972499", "GSM972500", "GSM972501", "GSM972502", "GSM972503", "GSM972504", "GSM972505", "GSM972506", "GSM972507", "GSM972508", "GSM972509", "GSM972510", "GSM972511", "GSM972512", "GSM972513", "GSM972514", "GSM972515", "GSM972516", "GSM972517", "GSM972518", "GSM972519", "GSM972520", "GSM972521", "GSM972522"], "sample_count": 585, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE132465 not downloaded", "asset:data:geo:GSE132465 licence not read", "asset:data:geo:GSE144735 not downloaded", "asset:data:geo:GSE144735 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "On the basis of log-rank testing, Kaplan–Meier curves were used to evaluate overall survival differences between different gene expression level groups."}}, {"id": "method-2", "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-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {"p_value": "elation coefficient and P-value are indicated"}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE132465", "GSE144735", "GSE39582"], "resolved_accessions": ["GSE132465", "GSE144735", "GSE39582"], "statements": ["Processed scRNA-seq count and transcripts per million (TPM) data of CRC samples were obtained from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database (http://www.ncbi.nlm.nih.gov/geo/) under accession codes GSE132465 (the Samsung Medical Center [SMC] dataset contains 63,689 cells from 23 primary CRC tissues and 10 matched normal mucosa tissues of 23 Korean CRC patients) and GSE144735 (the Katholieke Universiteit Leuven 3 [KUL3] dataset contains 27,414 cells from the core and border area of tumor regions as well as matched normal mucosa tissue of the six Belgian CRC patients)."], "basis": "The paper names GSE132465, GSE144735, GSE39582 in National Center for Biotechnology Information (NCBI) Gene Expression Omnibus database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:36914941", "data:geo:GSE132465"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE132465"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:33:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15858, "completion_tokens": 2964, "cached_tokens": 264}}, "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:36914941", "type": "paper", "label": "pmid:36914941"}, {"id": "source:pmid:36914941", "type": "manuscript", "label": "PMID 36914941 full text"}, {"id": "data:geo:GSE132465", "type": "dataset", "label": "GEO GSE132465"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36914941", "type": "paper", "label": "pmid:36914941"}, {"id": "source:pmid:36914941", "type": "manuscript", "label": "PMID 36914941 full text"}, {"id": "data:geo:GSE132465", "type": "dataset", "label": "GEO GSE132465"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36914941", "type": "extraction", "used": ["source:pmid:36914941"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE132465", "type": "accession_resolution", "used": ["data:geo:GSE132465"], "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:36914941", "parent_hash": "sha256:21b11602db9b4328732f8cc812c4e6f97e37532b2b3fd6851dc3dd29c4f2ca23", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE132465 licence not read", "asset:data:geo:GSE132465 not downloaded", "asset:data:geo:GSE144735 licence not read", "asset:data:geo:GSE144735 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["signatures. RESULTS: We employed single cell RNA-sequencing data to identify three types of tumor cells", "Methods Clinical sample collection and RNA sequencing Colorectal tumor tissue samples were collect", "as 8%. As all of the 24 MSS CRC patients had RNA sequencing data and clinical stage data, we used whole", "ith RNA integrity number > 7.0 were used for transcriptome sequencing with the Illumina NovaSeq6000 pla"], "order_basis": "paper_text_order:1256", "id": "assay:1"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["number status. Just like the grouping of the scRNA-seq data, we grouped chromosome 13 amplification", "py number status [Figure 4B]. Similar to the scRNA-seq dataset, SC1 had a higher CNV score than SC3"], "order_basis": "paper_text_order:4996", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["On the basis of log-rank testing, Kaplan–Meier curves were used to evaluate overall survival differences between different gene expression level groups."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T04:10:58+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}}}