{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31888570", "kind": "science-record", "revision": 6, "content_hash": "sha256:42d6331831a0f488611565a1658f50b5d1c4cb3f4c20d25b996ebba0699e4189", "created_at": "2026-11-01T15:40:54Z", "updated_at": "2026-11-01T21:22:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Downregulated SPINK4 is associated with poor survival in colorectal cancer.", "doi": "10.1186/s12885-019-6484-5", "pmid": "31888570", "authors": ["Xiaojie Wang", "Qian Yu", "Waleed M Ghareeb", "Yiyi Zhang", "Xingrong Lu", "Ying Huang", "Shenghui Huang", "Yanwu Sun", "Jiayi Lin", "Jin Liu", "Pan Chi"], "journal": "BMC cancer", "year": 2019, "abstract": "BACKGROUND: SPINK4 is known as a gastrointestinal peptide in the gastrointestinal tract and is abundantly expressed in human goblet cells. The clinical significance of SPINK4 in colorectal cancer (CRC) is largely unknown.\nMETHODS: We retrieved the expression data of 1168 CRC patients from 3 Gene Expression Omnibus (GEO) datasets (GSE24551, GSE39582, GSE32323) and The Cancer Genome Atlas (TCGA) to compare the expression level of SPINK4 between CRC tissues and normal colorectal tissues and to evaluate its value in predicting the survival of CRC patients. At the protein level, these results were further confirmed by data mining in the Human Protein Atlas and by immunohistochemical staining of samples from 81 CRC cases in our own center.\nRESULTS: SPINK4 expression was downregulated in CRC compared with that in normal tissues, and decreased SPINK4 expression at both the mRNA and protein levels was associated with poor prognosis in CRC patients from all 3 GEO datasets, the TCGA database and our cohort. Additionally, lower SPINK4 expression was significantly related to higher TNM stage. Moreover, in multivariate regression, SPINK4 was confirmed as an independent indicator of poor survival in CRC patients in all databases and in our own cohort.\nCONCLUSIONS: We concluded that reduced expression of SPINK4 relates to poor survival in CRC, functioning as a novel indicator.", "claims": [{"id": "claim-data-access", "statement": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31888570", "locator": "sections[24] \"Availability of data and materials\" paragraph 2", "quote": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/."}], "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:31888570"], "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:GSE24551"], "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:GSE24551"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31888570", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12885-019-6484-5", "sha256": "sha256:9a18cb8da304e7c1d4bdca7334cfb14ccf60fe08bbcf22c3e3bd0f3bf906d6a7", "bytes": 43048, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12885-019-6484-5", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6938003", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE24551", "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=GSE24551", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE24551", "version": null, "note": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM712082", "GSM712083", "GSM712084", "GSM712085", "GSM712086", "GSM712087", "GSM712088", "GSM712089", "GSM712090", "GSM712091", "GSM712092", "GSM712093", "GSM712094", "GSM712095", "GSM712096", "GSM712097", "GSM712098", "GSM712099", "GSM712100", "GSM712101", "GSM712102", "GSM712103", "GSM712104", "GSM712105", "GSM712106", "GSM712107", "GSM712108", "GSM712109", "GSM712110", "GSM712111", "GSM712112", "GSM712113", "GSM712114", "GSM712115", "GSM712116", "GSM712117", "GSM712118", "GSM712119", "GSM712120", "GSM712121", "GSM712122", "GSM712123", "GSM712124", "GSM712125", "GSM712126", "GSM712127", "GSM712128", "GSM712129", "GSM712130", "GSM712131", "GSM712132", "GSM712133", "GSM712134", "GSM712135", "GSM712136", "GSM712137", "GSM712138", "GSM712139", "GSM712140", "GSM712141", "GSM712142", "GSM712143", "GSM712144", "GSM712145", "GSM712146", "GSM712147", "GSM712148", "GSM712149", "GSM712150", "GSM712151", "GSM712152", "GSM712153", "GSM712154", "GSM712155", "GSM712156", "GSM712157", "GSM712158", "GSM712159", "GSM712160", "GSM712161", "GSM712162", "GSM712163", "GSM712164", "GSM712195", "GSM712196", "GSM712197", "GSM712198", "GSM712199", "GSM712200", "GSM712201", "GSM712202", "GSM712203", "GSM712204", "GSM712205", "GSM712206", "GSM712207", "GSM712208", "GSM712209", "GSM712210", "GSM712211", "GSM712212", "GSM712213", "GSM712214", "GSM712215", "GSM712216", "GSM712218", "GSM712221", "GSM712224", "GSM712226", "GSM712228", "GSM712231", "GSM712234", "GSM712237", "GSM712238", "GSM712241", "GSM712243", "GSM712245", "GSM712248", "GSM712251", "GSM712253", "GSM712255", "GSM712257", "GSM712258", "GSM712259", "GSM712260", "GSM712261", "GSM712262", "GSM712263", "GSM712264", "GSM712265", "GSM712266", "GSM712267", "GSM712268", "GSM712269", "GSM712270", "GSM712271", "GSM712272", "GSM712273", "GSM712274", "GSM712275", "GSM712276", "GSM712277", "GSM712278", "GSM712279", "GSM712280", "GSM712281", "GSM712282", "GSM712283", "GSM712284", "GSM712285", "GSM712286", "GSM712287", "GSM712288", "GSM712289", "GSM712290", "GSM712291", "GSM712292", "GSM712293", "GSM712294", "GSM712295", "GSM712296", "GSM712297", "GSM712298", "GSM712299", "GSM712300", "GSM712301", "GSM712398", "GSM712399", "GSM712400", "GSM712401", "GSM712402", "GSM712403", "GSM712404", "GSM712405", "GSM712406", "GSM712407", "GSM712408", "GSM712409", "GSM712410", "GSM712411", "GSM712412", "GSM712413", "GSM712414", "GSM712415", "GSM712416", "GSM712417", "GSM712418", "GSM712419", "GSM712420", "GSM712421", "GSM712422", "GSM712423", "GSM712424", "GSM712425", "GSM712426", "GSM712427", "GSM712428", "GSM712429", "GSM712430", "GSM712431", "GSM712432", "GSM712433", "GSM712434", "GSM712435", "GSM712436", "GSM712437", "GSM712438", "GSM712439", "GSM712440", "GSM712441", "GSM712442", "GSM712443", "GSM712444", "GSM712445", "GSM712446", "GSM712447", "GSM712448", "GSM712449", "GSM712450", "GSM712451", "GSM712452", "GSM712453", "GSM712454", "GSM712455", "GSM712456", "GSM712457", "GSM712458", "GSM712459", "GSM712460", "GSM712461", "GSM712462", "GSM712463", "GSM712464", "GSM712465", "GSM712466", "GSM712467", "GSM712468", "GSM712469", "GSM712470", "GSM712471", "GSM712472", "GSM712473", "GSM712474", "GSM712573", "GSM712574", "GSM712575", "GSM712576", "GSM712577", "GSM712578", "GSM712579", "GSM712580", "GSM712581", "GSM712582", "GSM712583", "GSM712584", "GSM712585", "GSM712586", "GSM712587", "GSM712588", "GSM712589", "GSM712590", "GSM712591", "GSM712592", "GSM712593", "GSM712594", "GSM712595", "GSM712596", "GSM712597", "GSM712598", "GSM712599", "GSM712600", "GSM712601", "GSM712602", "GSM712603", "GSM712604", "GSM712605", "GSM712606", "GSM712607", "GSM712608", "GSM712609", "GSM712610", "GSM712611", "GSM712612", "GSM712613", "GSM712614", "GSM712615", "GSM712616", "GSM712617", "GSM712618", "GSM712619", "GSM712620", "GSM712621", "GSM712622", "GSM712623", "GSM712624", "GSM712625", "GSM712626", "GSM712627", "GSM712628", "GSM712629", "GSM712630", "GSM712631", "GSM712632", "GSM712633", "GSM712634", "GSM712635", "GSM712636", "GSM712637", "GSM712638", "GSM712639", "GSM712640", "GSM712641", "GSM712642", "GSM712643", "GSM712644", "GSM712645", "GSM712646", "GSM712647", "GSM712648", "GSM712649", "GSM714419", "GSM714420", "GSM714421", "GSM714422", "GSM714423", "GSM714424", "GSM714425", "GSM714426", "GSM714427", "GSM714428", "GSM714429", "GSM714430", "GSM714431"], "sample_count": 333, "group_sizes": null, "group_sizes_basis": null, "platform": "5175;11028", "taxon": "Homo sapiens", "title": "Exon level expression profiling of colorectal cancer tissue samples", "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:GSE32323", "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=GSE32323", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32323", "version": null, "note": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM800742", "GSM800743", "GSM800744", "GSM800745", "GSM800746", "GSM800747", "GSM800748", "GSM800749", "GSM800750", "GSM800751", "GSM800752", "GSM800753", "GSM800754", "GSM800755", "GSM800756", "GSM800757", "GSM800758", "GSM800759", "GSM800760", "GSM800761", "GSM800762", "GSM800763", "GSM800764", "GSM800765", "GSM800766", "GSM800767", "GSM800768", "GSM800769", "GSM800770", "GSM800771", "GSM800772", "GSM800773", "GSM800774", "GSM800775", "GSM800776", "GSM800777", "GSM800778", "GSM800779", "GSM800780", "GSM800781", "GSM800782", "GSM800783", "GSM800784", "GSM800785"], "sample_count": 44, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Screening for Epigenetically Masked Genes in Colorectal Cancer using 5-aza-2’-deoxycytidine treatment, Microarray and Gene Expression Profile", "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:GSE3880", "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=GSE3880", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE3880", "version": null, "note": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM88316", "GSM88317", "GSM88318", "GSM88319", "GSM88320", "GSM88321", "GSM88322", "GSM88323"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "1818", "taxon": "Homo sapiens", "title": "Gene expression profiling in colonic adenoma and carcinoma in situ", "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: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": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "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}}, {"id": "data:geo:GSE81861", "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=GSE81861", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE81861", "version": null, "note": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2180156", "GSM2180157", "GSM2180158", "GSM2180159", "GSM2180160", "GSM2180161", "GSM2180162", "GSM2180163", "GSM2180164", "GSM2180165", "GSM2180166", "GSM2180167", "GSM2180168", "GSM2180169", "GSM2180170", "GSM2180171", "GSM2180172", "GSM2180173", "GSM2180174", "GSM2180175", "GSM2180176", "GSM2180177", "GSM2180178", "GSM2180179", "GSM2180180", "GSM2180181", "GSM2180182", "GSM2180183", "GSM2180184", "GSM2180185", "GSM2180186", "GSM2180187", "GSM2180188", "GSM2180189", "GSM2180190", "GSM2180191", "GSM2180192", "GSM2180193", "GSM2180194", "GSM2180195", "GSM2180196", "GSM2180197", "GSM2180198", "GSM2180199", "GSM2180200", "GSM2180201", "GSM2180202", "GSM2180203", "GSM2180204", "GSM2180205", "GSM2180206", "GSM2180207", "GSM2180208", "GSM2180209", "GSM2180210", "GSM2180211", "GSM2180212", "GSM2180213", "GSM2180214", "GSM2180215", "GSM2180216", "GSM2180217", "GSM2180218", "GSM2180219", "GSM2180220", "GSM2180221", "GSM2180222", "GSM2180223", "GSM2180224", "GSM2180225", "GSM2180226", "GSM2180227", "GSM2180228", "GSM2180229", "GSM2180230", "GSM2180231", "GSM2180232", "GSM2180233", "GSM2180234", "GSM2180235", "GSM2180236", "GSM2180237", "GSM2180238", "GSM2180239", "GSM2180240", "GSM2180241", "GSM2180242", "GSM2180243", "GSM2180244", "GSM2180245", "GSM2180246", "GSM2180247", "GSM2180248", "GSM2180249", "GSM2180250", "GSM2180251", "GSM2180252", "GSM2180253", "GSM2180254", "GSM2180255", "GSM2180256", "GSM2180257", "GSM2180258", "GSM2180259", "GSM2180260", "GSM2180261", "GSM2180262", "GSM2180263", "GSM2180264", "GSM2180265", "GSM2180266", "GSM2180267", "GSM2180268", "GSM2180269", "GSM2180270", "GSM2180271", "GSM2180272", "GSM2180273", "GSM2180274", "GSM2180275", "GSM2180276", "GSM2180277", "GSM2180278", "GSM2180279", "GSM2180280", "GSM2180281", "GSM2180282", "GSM2180283", "GSM2180284", "GSM2180285", "GSM2180286", "GSM2180287", "GSM2180288", "GSM2180289", "GSM2180290", "GSM2180291", "GSM2180292", "GSM2180293", "GSM2180294", "GSM2180295", "GSM2180296", "GSM2180297", "GSM2180298", "GSM2180299", "GSM2180300", "GSM2180301", "GSM2180302", "GSM2180303", "GSM2180304", "GSM2180305", "GSM2180306", "GSM2180307", "GSM2180308", "GSM2180309", "GSM2180310", "GSM2180311", "GSM2180312", "GSM2180313", "GSM2180314", "GSM2180315", "GSM2180316", "GSM2180317", "GSM2180318", "GSM2180319", "GSM2180320", "GSM2180321", "GSM2180322", "GSM2180323", "GSM2180324", "GSM2180325", "GSM2180326", "GSM2180327", "GSM2180328", "GSM2180329", "GSM2180330", "GSM2180331", "GSM2180332", "GSM2180333", "GSM2180334", "GSM2180335", "GSM2180336", "GSM2180337", "GSM2180338", "GSM2180339", "GSM2180340", "GSM2180341", "GSM2180342", "GSM2180343", "GSM2180344", "GSM2180345", "GSM2180346", "GSM2180347", "GSM2180348", "GSM2180349", "GSM2180350", "GSM2180351", "GSM2180352", "GSM2180353", "GSM2180354", "GSM2180355", "GSM2180356", "GSM2180357", "GSM2180358", "GSM2180359", "GSM2180360", "GSM2180361", "GSM2180362", "GSM2180363", "GSM2180364", "GSM2180365", "GSM2180366", "GSM2180367", "GSM2180368", "GSM2180369", "GSM2180370", "GSM2180371", "GSM2180372", "GSM2180373", "GSM2180374", "GSM2180375", "GSM2180376", "GSM2180377", "GSM2180378", "GSM2180379", "GSM2180380", "GSM2180381", "GSM2180382", "GSM2180383", "GSM2180384", "GSM2180385", "GSM2180386", "GSM2180387", "GSM2180388", "GSM2180389", "GSM2180390", "GSM2180391", "GSM2180392", "GSM2180393", "GSM2180394", "GSM2180395", "GSM2180396", "GSM2180397", "GSM2180398", "GSM2180399", "GSM2180400", "GSM2180401", "GSM2180402", "GSM2180403", "GSM2180404", "GSM2180405", "GSM2180406", "GSM2180407", "GSM2180408", "GSM2180409", "GSM2180410", "GSM2180411", "GSM2180412", "GSM2180413", "GSM2180414", "GSM2180415", "GSM2180416", "GSM2180417", "GSM2180418", "GSM2180419", "GSM2180420", "GSM2180421", "GSM2180422", "GSM2180423", "GSM2180424", "GSM2180425", "GSM2180426", "GSM2180427", "GSM2180428", "GSM2180429", "GSM2180430", "GSM2180431", "GSM2180432", "GSM2180433", "GSM2180434", "GSM2180435", "GSM2180436", "GSM2180437", "GSM2180438", "GSM2180439", "GSM2180440", "GSM2180441", "GSM2180442", "GSM2180443", "GSM2180444", "GSM2180445", "GSM2180446", "GSM2180447", "GSM2180448", "GSM2180449", "GSM2180450", "GSM2180451", "GSM2180452", "GSM2180453", "GSM2180454", "GSM2180455", "GSM2180456", "GSM2180457", "GSM2180458", "GSM2180459", "GSM2180460", "GSM2180461", "GSM2180462", "GSM2180463", "GSM2180464", "GSM2180465", "GSM2180466", "GSM2180467", "GSM2180468", "GSM2180469", "GSM2180470", "GSM2180471", "GSM2180472", "GSM2180473", "GSM2180474", "GSM2180475", "GSM2180476", "GSM2180477", "GSM2180478", "GSM2180479", "GSM2180480", "GSM2180481", "GSM2180482", "GSM2180483", "GSM2180484", "GSM2180485", "GSM2180486", "GSM2180487", "GSM2180488", "GSM2180489", "GSM2180490", "GSM2180491", "GSM2180492", "GSM2180493", "GSM2180494", "GSM2180495", "GSM2180496", "GSM2180497", "GSM2180498", "GSM2180499", "GSM2180500", "GSM2180501", "GSM2180502", "GSM2180503", "GSM2180504", "GSM2180505", "GSM2180506", "GSM2180507", "GSM2180508", "GSM2180509", "GSM2180510", "GSM2180511", "GSM2180512", "GSM2180513", "GSM2180514", "GSM2180515", "GSM2180516", "GSM2180517", "GSM2180518", "GSM2180519", "GSM2180520", "GSM2180521", "GSM2180522", "GSM2180523", "GSM2180524", "GSM2180525", "GSM2180526", "GSM2180527", "GSM2180528", "GSM2180529", "GSM2180530", "GSM2180531", "GSM2180532", "GSM2180533", "GSM2180534", "GSM2180535", "GSM2180536", "GSM2180537", "GSM2180538", "GSM2180539", "GSM2180540", "GSM2180541", "GSM2180542", "GSM2180543", "GSM2180544", "GSM2180545", "GSM2180546", "GSM2180547", "GSM2180548", "GSM2180549", "GSM2180550", "GSM2180551", "GSM2180552", "GSM2180553", "GSM2180554", "GSM2180555", "GSM2180556", "GSM2180557", "GSM2180558", "GSM2180559", "GSM2180560", "GSM2180561", "GSM2180562", "GSM2180563", "GSM2180564", "GSM2180565", "GSM2180566", "GSM2180567", "GSM2180568", "GSM2180569", "GSM2180570", "GSM2180571", "GSM2180572", "GSM2180573", "GSM2180574", "GSM2180575", "GSM2180576", "GSM2180577", "GSM2180578", "GSM2180579", "GSM2180580", "GSM2180581", "GSM2180582", "GSM2180583", "GSM2180584", "GSM2180585", "GSM2180586", "GSM2180587", "GSM2180588", "GSM2180589", "GSM2180590", "GSM2180591", "GSM2180592", "GSM2180593", "GSM2180594", "GSM2180595", "GSM2180596", "GSM2180597", "GSM2180598", "GSM2180599", "GSM2180600", "GSM2180601", "GSM2180602", "GSM2180603", "GSM2180604", "GSM2180605", "GSM2180606", "GSM2180607", "GSM2180608", "GSM2180609", "GSM2180610", "GSM2180611", "GSM2180612", "GSM2180613", "GSM2180614", "GSM2180615", "GSM2180616", "GSM2180617", "GSM2180618", "GSM2180619", "GSM2180620", "GSM2180621", "GSM2180622", "GSM2180623", "GSM2180624", "GSM2180625", "GSM2180626", "GSM2180627", "GSM2180628", "GSM2180629", "GSM2180630", "GSM2180631", "GSM2180632", "GSM2180633", "GSM2180634", "GSM2180635", "GSM2180636", "GSM2180637", "GSM2180638", "GSM2180639", "GSM2180640", "GSM2180641", "GSM2180642", "GSM2180643", "GSM2180644", "GSM2180645", "GSM2180646", "GSM2180647", "GSM2180648", "GSM2180649", "GSM2180650", "GSM2180651", "GSM2180652", "GSM2180653", "GSM2180654", "GSM2180655", "GSM2180656", "GSM2180657", "GSM2180658", "GSM2180659", "GSM2180660", "GSM2180661", "GSM2180662", "GSM2180663", "GSM2180664", "GSM2180665", "GSM2180666", "GSM2180667", "GSM2180668", "GSM2180669", "GSM2180670", "GSM2180671", "GSM2180672", "GSM2180673", "GSM2180674", "GSM2180675", "GSM2180676", "GSM2180677", "GSM2180678", "GSM2180679", "GSM2180680", "GSM2180681", "GSM2180682", "GSM2180683", "GSM2180684", "GSM2180685", "GSM2180686", "GSM2180687", "GSM2180688", "GSM2180689", "GSM2180690", "GSM2180691", "GSM2180692", "GSM2180693", "GSM2180694", "GSM2180695", "GSM2180696", "GSM2180697", "GSM2180698", "GSM2180699", "GSM2180700", "GSM2180701", "GSM2180702", "GSM2180703", "GSM2180704", "GSM2180705", "GSM2180706", "GSM2180707", "GSM2180708", "GSM2180709", "GSM2180710", "GSM2180711", "GSM2180712", "GSM2180713", "GSM2180714", "GSM2180715", "GSM2180716", "GSM2180717", "GSM2180718", "GSM2180719", "GSM2180720", "GSM2180721", "GSM2180722", "GSM2180723", "GSM2180724", "GSM2180725", "GSM2180726", "GSM2180727", "GSM2180728", "GSM2180729", "GSM2180730", "GSM2180731", "GSM2180732", "GSM2180733", "GSM2180734", "GSM2180735", "GSM2180736", "GSM2180737", "GSM2180738", "GSM2180739", "GSM2180740", "GSM2180741", "GSM2180742", "GSM2180743", "GSM2180744", "GSM2180745", "GSM2180746", "GSM2180747", "GSM2180748", "GSM2180749", "GSM2180750", "GSM2180751", "GSM2180752", "GSM2180753", "GSM2180754", "GSM2180755", "GSM2180756", "GSM2180757", "GSM2180758", "GSM2180759", "GSM2180760", "GSM2180761", "GSM2180762", "GSM2180763", "GSM2180764", "GSM2180765", "GSM2180766", "GSM2180767", "GSM2180768", "GSM2180769", "GSM2180770", "GSM2180771", "GSM2180772", "GSM2180773", "GSM2180774", "GSM2180775", "GSM2180776", "GSM2180777", "GSM2180778", "GSM2180779", "GSM2180780", "GSM2180781", "GSM2180782", "GSM2180783", "GSM2180784", "GSM2180785", "GSM2180786", "GSM2180787", "GSM2180788", "GSM2180789", "GSM2180790", "GSM2180791", "GSM2180792", "GSM2180793", "GSM2180794", "GSM2180795", "GSM2180796", "GSM2180797", "GSM2180798", "GSM2180799", "GSM2180800", "GSM2180801", "GSM2180802", "GSM2180803", "GSM2180804", "GSM2180805", "GSM2180806", "GSM2180807", "GSM2180808", "GSM2180809", "GSM2180810", "GSM2180811", "GSM2180812", "GSM2180813", "GSM2180814", "GSM2180815", "GSM2180816", "GSM2180817", "GSM2180818", "GSM2180819", "GSM2180820", "GSM2180821", "GSM2180822", "GSM2180823", "GSM2180824", "GSM2180825", "GSM2180826", "GSM2180827", "GSM2180828", "GSM2180829", "GSM2180830", "GSM2180831", "GSM2180832", "GSM2180833", "GSM2180834", "GSM2180835", "GSM2180836", "GSM2180837", "GSM2180838", "GSM2180839", "GSM2180840", "GSM2180841", "GSM2180842", "GSM2180843", "GSM2180844", "GSM2180845", "GSM2180846", "GSM2180847", "GSM2180848", "GSM2180849", "GSM2180850", "GSM2180851", "GSM2180852", "GSM2180853", "GSM2180854", "GSM2180855", "GSM2180856", "GSM2180857", "GSM2180858", "GSM2180859", "GSM2180860", "GSM2180861", "GSM2180862", "GSM2180863", "GSM2180864", "GSM2180865", "GSM2180866", "GSM2180867", "GSM2180868", "GSM2180869", "GSM2180870", "GSM2180871", "GSM2180872", "GSM2180873", "GSM2180874", "GSM2180875", "GSM2180876", "GSM2180877", "GSM2180878", "GSM2180879", "GSM2180880", "GSM2180881", "GSM2180882", "GSM2180883", "GSM2180884", "GSM2180885", "GSM2180886", "GSM2180887", "GSM2180888", "GSM2180889", "GSM2180890", "GSM2180891", "GSM2180892", "GSM2180893", "GSM2180894", "GSM2180895", "GSM2180896", "GSM2180897", "GSM2180898", "GSM2180899", "GSM2180900", "GSM2180901", "GSM2180902", "GSM2180903", "GSM2180904", "GSM2180905", "GSM2180906", "GSM2180907", "GSM2180908", "GSM2180909", "GSM2180910", "GSM2180911", "GSM2180912", "GSM2180913", "GSM2180914", "GSM2180915", "GSM2180916", "GSM2180917", "GSM2180918", "GSM2180919", "GSM2180920", "GSM2180921", "GSM2180922", "GSM2180923", "GSM2180924", "GSM2180925", "GSM2180926", "GSM2180927", "GSM2180928", "GSM2180929", "GSM2180930", "GSM2180931", "GSM2180932", "GSM2180933", "GSM2180934", "GSM2180935", "GSM2180936", "GSM2180937", "GSM2180938", "GSM2180939", "GSM2180940", "GSM2180941", "GSM2180942", "GSM2180943", "GSM2180944", "GSM2180945", "GSM2180946", "GSM2180947", "GSM2180948", "GSM2180949", "GSM2180950", "GSM2180951", "GSM2180952", "GSM2180953", "GSM2180954", "GSM2180955", "GSM2180956", "GSM2180957", "GSM2180958", "GSM2180959", "GSM2180960", "GSM2180961", "GSM2180962", "GSM2180963", "GSM2180964", "GSM2180965", "GSM2180966", "GSM2180967", "GSM2180968", "GSM2180969", "GSM2180970", "GSM2180971", "GSM2180972", "GSM2180973", "GSM2180974", "GSM2180975", "GSM2180976", "GSM2180977", "GSM2180978", "GSM2180979", "GSM2180980", "GSM2180981", "GSM2180982", "GSM2180983", "GSM2180984", "GSM2180985", "GSM2180986", "GSM2180987", "GSM2180988", "GSM2180989", "GSM2180990", "GSM2180991", "GSM2180992", "GSM2180993", "GSM2180994", "GSM2180995", "GSM2180996", "GSM2180997", "GSM2180998", "GSM2180999", "GSM2181000", "GSM2181001", "GSM2181002", "GSM2181003", "GSM2181004", "GSM2181005", "GSM2181006", "GSM2181007", "GSM2181008", "GSM2181009", "GSM2181010", "GSM2181011", "GSM2181012", "GSM2181013", "GSM2181014", "GSM2181015", "GSM2181016", "GSM2181017", "GSM2181018", "GSM2181019", "GSM2181020", "GSM2181021", "GSM2181022", "GSM2181023", "GSM2181024", "GSM2181025", "GSM2181026", "GSM2181027", "GSM2181028", "GSM2181029", "GSM2181030", "GSM2181031", "GSM2181032", "GSM2181033", "GSM2181034", "GSM2181035", "GSM2181036", "GSM2181037", "GSM2181038", "GSM2181039", "GSM2181040", "GSM2181041", "GSM2181042", "GSM2181043", "GSM2181044", "GSM2181045", "GSM2181046", "GSM2181047", "GSM2181048", "GSM2181049", "GSM2181050", "GSM2181051", "GSM2181052", "GSM2181053", "GSM2181054", "GSM2181055", "GSM2181056", "GSM2181057", "GSM2181058", "GSM2181059", "GSM2181060", "GSM2181061", "GSM2181062", "GSM2181063", "GSM2181064", "GSM2181065", "GSM2181066", "GSM2181067", "GSM2181068", "GSM2181069", "GSM2181070", "GSM2181071", "GSM2181072", "GSM2181073", "GSM2181074", "GSM2181075", "GSM2181076", "GSM2181077", "GSM2181078", "GSM2181079", "GSM2181080", "GSM2181081", "GSM2181082", "GSM2181083", "GSM2181084", "GSM2181085", "GSM2181086", "GSM2181087", "GSM2181088", "GSM2181089", "GSM2181090", "GSM2181091", "GSM2181092", "GSM2181093", "GSM2181094", "GSM2181095", "GSM2181096", "GSM2181097", "GSM2181098", "GSM2181099", "GSM2181100", "GSM2181101", "GSM2181102", "GSM2181103", "GSM2181104", "GSM2181105", "GSM2181106", "GSM2181107", "GSM2181108", "GSM2181109", "GSM2181110", "GSM2181111", "GSM2181112", "GSM2181113", "GSM2181114", "GSM2181115", "GSM2181116", "GSM2181117", "GSM2181118", "GSM2181119", "GSM2181120", "GSM2181121", "GSM2181122", "GSM2181123", "GSM2181124", "GSM2181125", "GSM2181126", "GSM2181127", "GSM2181128", "GSM2181129", "GSM2181130", "GSM2181131", "GSM2181132", "GSM2181133", "GSM2181134", "GSM2181135", "GSM2181136", "GSM2181137", "GSM2181138", "GSM2181139", "GSM2181140", "GSM2181141", "GSM2181142", "GSM2181143", "GSM2181144", "GSM2181145", "GSM2181146", "GSM2181147", "GSM2181148", "GSM2181149", "GSM2181150", "GSM2181151", "GSM2181152", "GSM2181153", "GSM2181154", "GSM2181155", "GSM2181156", "GSM2181157", "GSM2181158", "GSM2181159", "GSM2181160", "GSM2181161", "GSM2181162", "GSM2181163", "GSM2181164", "GSM2181165", "GSM2181166", "GSM2181167", "GSM2181168", "GSM2181169", "GSM2181170", "GSM2181171", "GSM2181172", "GSM2181173", "GSM2181174", "GSM2181175", "GSM2181176", "GSM2181177", "GSM2181178", "GSM2181179", "GSM2181180", "GSM2181181", "GSM2181182", "GSM2181183", "GSM2181184", "GSM2181185", "GSM2181186", "GSM2181187", "GSM2181188", "GSM2181189", "GSM2181190", "GSM2181191", "GSM2181192", "GSM2181193", "GSM2181194", "GSM2181195", "GSM2181196", "GSM2181197", "GSM2181198", "GSM2181199", "GSM2181200", "GSM2181201", "GSM2181202", "GSM2181203", "GSM2181204", "GSM2181205", "GSM2181206", "GSM2181207", "GSM2181208", "GSM2181209", "GSM2181210", "GSM2181211", "GSM2181212", "GSM2181213", "GSM2181214", "GSM2181215", "GSM2181216", "GSM2181217", "GSM2181218", "GSM2181219", "GSM2181220", "GSM2181221", "GSM2181222", "GSM2181223", "GSM2181224", "GSM2181225", "GSM2181226", "GSM2181227", "GSM2181228", "GSM2181229", "GSM2181230", "GSM2181231", "GSM2181232", "GSM2181233", "GSM2181234", "GSM2181235", "GSM2181236", "GSM2181237", "GSM2181238", "GSM2181239", "GSM2181240", "GSM2181241", "GSM2181242", "GSM2181243", "GSM2181244", "GSM2181245", "GSM2181246", "GSM2181247", "GSM2181248", "GSM2181249", "GSM2181250", "GSM2181251", "GSM2181252", "GSM2181253", "GSM2181254", "GSM2181255", "GSM2181256", "GSM2181257", "GSM2181258", "GSM2181259", "GSM2181260", "GSM2181261", "GSM2181262", "GSM2181263", "GSM2181264", "GSM2181265", "GSM2181266", "GSM2181267", "GSM2181268", "GSM2181269", "GSM2181270", "GSM2181271", "GSM2181272", "GSM2181273", "GSM2181274", "GSM2181275", "GSM2181276", "GSM2181277", "GSM2181278", "GSM2181279", "GSM2181280", "GSM2181281", "GSM2181282", "GSM2181283", "GSM2181284", "GSM2181285", "GSM2181286", "GSM2181287", "GSM2181288", "GSM2181289", "GSM2181290", "GSM2181291", "GSM2181292", "GSM2181293", "GSM2181294", "GSM2181295", "GSM2181296", "GSM2181297", "GSM2181298", "GSM2181299", "GSM2181300", "GSM2181301", "GSM2181302", "GSM2181303", "GSM2181304", "GSM2181305", "GSM2181306", "GSM2181307", "GSM2181308", "GSM2181309", "GSM2181310", "GSM2181311", "GSM2181312", "GSM2181313", "GSM2181314", "GSM2181315", "GSM2181316", "GSM2181317", "GSM2181318", "GSM2181319", "GSM2181320", "GSM2181321", "GSM2181322", "GSM2181323", "GSM2181324", "GSM2181325", "GSM2181326", "GSM2181327", "GSM2181328", "GSM2181329", "GSM2181330", "GSM2181331", "GSM2181332", "GSM2181333", "GSM2181334", "GSM2181335", "GSM2181336", "GSM2181337", "GSM2181338", "GSM2181339", "GSM2181340", "GSM2181341", "GSM2181342", "GSM2181343", "GSM2181344", "GSM2181345", "GSM2181346", "GSM2181347", "GSM2181348", "GSM2181349", "GSM2181350", "GSM2181351", "GSM2181352", "GSM2181353", "GSM2181354", "GSM2181355", "GSM2181356", "GSM2181357", "GSM2181358", "GSM2181359", "GSM2181360", "GSM2181361", "GSM2181362", "GSM2181363", "GSM2181364", "GSM2181365", "GSM2181366", "GSM2181367", "GSM2181368", "GSM2181369", "GSM2181370", "GSM2181371", "GSM2181372", "GSM2181373", "GSM2181374", "GSM2181375"], "sample_count": 1220, "group_sizes": null, "group_sizes_basis": null, "platform": "11154", "taxon": "Homo sapiens", "title": "Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31888570:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:342db1649defb20e9472f01ee3808012eeb36f6f6c59d8ca9973ab3cec0f225e", "bytes": 1411, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#Tab1", "version": null, "note": "Correlations between SPINK4 expression and the clinicopathological features of patients with CRC in our own study cohort", "structure": {"pmcid": "PMC6938003", "section_index": 13, "section_title": "Correlations between SPINK4 expression and clinicopathological characteristics", "row_count": 24, "column_count": 6}, "table": {"label": "Table 1", "caption": "Correlations between SPINK4 expression and the clinicopathological features of patients with CRC in our own study cohort", "rows": [["", "Low expression", "High expression", "P value"], ["Gender", "0.405"], ["Male", "28", "(50.0)", "15", "(60.0)", ""], ["Female", "28", "(50.0)", "10", "(40.0)", ""], ["Age (years)", "63.3 ± 12.4", "", "64.1 ± 12.1", "", "0.809"], ["BMI (kg/m2)", "22.0 ± 3.4", "", "23.9 ± 2.5", "", "0.031"], ["TNM stage", "0.025"], ["I-II", "23", "(41.1)", "17", "(68.0)", ""], ["III-IV", "33", "(58.9)", "8", "(32.0)", ""], ["Tumor size (cm)", "5.0 ± 2.0", "", "4.1 ± 1.6", "", "0.075"], ["Histological type", "0.366"], ["Adenocarcinoma", "53", "(94.6)", "22", "(88.0)", ""], ["Mucinous adenocarcinoma", "3", "(5.4)", "3", "(12.0)", "0.306"], ["Pretreatment CEA level (ng/mL)", "11.1 ± 22.1", "", "11.4 ± 22.1", "", "0.953"], ["Pretreatment CA199 level (U/ml)", "32.8 ± 75.3", "", "17.5 ± 17.9", "", "0.319"], ["Perineural invasion", "4", "(7.1)", "0", "(0.0)", ""], ["Venus invasion", "8", "(14.3)", "3", "(12.0)", "1.000"], ["Tumor location", "0.874"], ["Left colon", "5", "(8.9)", "3", "(12.0)", ""], ["Right colon", "19", "(33.9)", "9", "(36.0)", ""], ["Rectum", "32", "(57.1)", "13", "(52.0)", ""], ["Tumor grade", "0.583"], ["Well to moderately differentiated", "54", "(96.4)", "23", "(92.0)", ""], ["Poorly differentiated", "2", "(3.6)", "2", "(8.0)", ""]], "row_count": 24, "column_count": 6, "numeric_cells": 75, "header_rows": 1, "locator": "section[13]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31888570:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e503a69f31b5c3243106e57c8bfb62519dc94116687d12d2b0a6b2fcca26d2c4", "bytes": 1786, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#Tab2", "version": null, "note": "Clinical characteristics of patients in GSE24551, GSE39582 and TCGA database", "structure": {"pmcid": "PMC6938003", "section_index": 14, "section_title": "Correlations between SPINK4 expression and CRC patient survival", "row_count": 48, "column_count": 5}, "table": {"label": "Table 2", "caption": "Clinical characteristics of patients in GSE24551, GSE39582 and TCGA database", "rows": [["Datasets", "Characteristics", "", "Values", ""], ["GSE24551 dataset", "TNM stage", "II", "90", "(56.3)"], ["", "III", "70", "(43.8)"], ["Microsatellite status", "MSS, MSI-L", "126", "(78.8)"], ["", "MSI-H", "21", "(13.1)"], ["", "Missing", "13", "(8.1)"], ["GSE39582 dataset", "Gender", "Male", "288", "(54.5)"], ["", "Female", "240", "(45.5)"], ["Age (years)", "", "66.6 ± 13.4", ""], ["TNM stage", "0", "4", "(0.8)"], ["", "I", "32", "(6.1)"], ["", "II", "246", "(46.6)"], ["", "III", "188", "(35.6)"], ["", "IV", "58", "(11.0)"], ["BRAF status", "WT", "431", "(81.6)"], ["", "MT", "47", "(8.9)"], ["", "Missing", "50", "(9.5)"], ["KRAS status", "WT", "305", "(57.8)"], ["", "MT", "202", "(38.3)"], ["", "Missing", "21", "(4.0)"], ["TP53 status", "WT", "148", "(28.0)"], ["", "MT", "174", "(33.0)"], ["", "Missing", "206", "(39.0)"], ["MMR status", "pMMR", "413", "(78.2)"], ["", "dMMR", "69", "(13.1)"], ["", "Missing", "46", "(8.7)"], ["TCGA database", "Gender", "Male", "234", "(53.4)"], ["", "Female", "204", "(46.6)"], ["Age (years)", "", "66.6 ± 13.0", ""], ["TNM stage", "I", "73", "(16.7)"], ["", "II", "194", "(44.3)"], ["", "III", "99", "(22.6)"], ["", "IV", "61", "(13.9)"], ["", "Missing", "11", "(2.5)"], ["Pretreatment CEA level", "", "", ""], ["(ng/ml)", "38.4 ± 201.3", "", ""], ["Histological type", "Adenocarcinoma", "373", "(85.2)"], ["", "Mucinous adenocarcinoma", "60", "(13.7)"], ["", "Missing", "5", "(1.1)"], ["Perineural invasion", "No", "131", "(29.9)"], ["", "Yes", "45", "(10.3)"], ["", "Missing", "262", "(59.8)"], ["Tumor deposits", "No", "184", "(42.0)"], ["", "Yes", "38", "(8.7)"], ["", "Missing", "216", "(49.3)"], ["KRAS status", "WT", "24", "(5.5)"], ["", "MT", "22", "(5.0)"], ["", "Missing", "392", "(89.5)"]], "row_count": 48, "column_count": 5, "numeric_cells": 93, "header_rows": 1, "locator": "section[14]/table-wrap[1]#Tab2"}}, {"id": "asset:table:pmid:31888570:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7d1d3d5906176713ac903b79ad4ab3fcc3d9385104ab68ba0d035e4146687b1c", "bytes": 2895, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[2]#Tab3", "version": null, "note": "Multivariate analysis of indicators for overall survival in CRC patients in GSE24551, GSE39582 and TCGA database", "structure": {"pmcid": "PMC6938003", "section_index": 14, "section_title": "Correlations between SPINK4 expression and CRC patient survival", "row_count": 41, "column_count": 7}, "table": {"label": "Table 3", "caption": "Multivariate analysis of indicators for overall survival in CRC patients in GSE24551, GSE39582 and TCGA database", "rows": [["Datasets", "Variable", "Group", "HR", "(95% CI)", "", "P value"], ["GSE24551 dataset", "Univariate analysis", "", "", "", "", ""], ["TNM stage", "(III vs. II)", "1.966", "1.190", "3.246", "0.008"], ["Microsatellite status", "(MSI-H vs. MSS, MSI-L)", "0.246", "0.077", "0.786", "0.018"], ["SPINK4 expression", "(high vs. low)", "0.413", "0.188", "0.906", "0.027"], ["Multivariate analysis", "", "", "", "", ""], ["TNM stage", "(III vs. II)", "1.977", "1.181", "3.310", "0.010"], ["Microsatellite status", "(MSI-H vs. MSS, MSI-L)", "0.231", "0.072", "0.738", "0.013"], ["SPINK4 expression", "(high vs. low)", "0.462", "0.210", "1.018", "0.056"], ["GSE39582 dataset", "Univariate analysis", "", "", "", "", ""], ["Gender", "(female vs. male)", "0.773", "0.569", "1.051", "0.100"], ["Age", "(per year)", "1.024", "1.011", "1.037", "0.000"], ["TNM stage", "(III-IV vs. I-II)", "2.033", "1.644", "2.513", "0.000"], ["MMR status", "(dMMR vs. pMMR)", "0.808", "0.488", "1.340", "0.410"], ["TP53 status", "(MT vs. WT)", "1.290", "0.884", "1.883", "0.187"], ["KRAS status", "(MT vs. WT)", "1.347", "0.989", "1.834", "0.059"], ["BRAF status", "(MT vs. WT)", "1.162", "0.681", "1.982", "0.582"], ["SPINK4 expression", "(high vs. low)", "0.662", "0.464", "0.944", "0.023"], ["Multivariate analysis", "", "", "", "", ""], ["Age", "(per year)", "1.025", "1.012", "1.039", "0.000"], ["TNM stage", "(III-IV vs. I-II)", "1.921", "1.406", "2.625", "0.000"], ["KRAS status", "(MT vs. WT)", "1.365", "1.001", "1.861", "0.050"], ["SPINK4 expression", "(high vs. low)", "0.636", "0.444", "0.911", "0.014"], ["TCGA dataset", "Univariate analysis", "", "", "", "", ""], ["Gender", "(female vs. male)", "0.884", "0.593", "1.318", "0.545"], ["Age", "(per year)", "1.018", "1.002", "1.035", "0.030"], ["TNM stage", "(III-IV vs. I-II)", "3.002", "1.979", "4.554", "0.000"], ["KRAS status", "(MT vs. WT)", "1.416", "0.610", "3.288", "0.418"], ["Tumor deposits", "(yes vs. No)", "1.752", "0.854", "3.594", "0.126"], ["Perineural invasion", "(yes vs. No)", "1.938", "0.981", "3.826", "0.057"], ["Venus invasion", "(yes vs. No)", "2.566", "1.658", "3.970", "0.000"], ["Pretreatment CEA level", "(per ng/mL)", "1.001", "1.001", "1.002", "0.000"], ["Lymphatic invasion", "(yes vs. No)", "2.140", "1.393", "3.287", "0.001"], ["Histological type", "(mucinous adenocarcinoma vs. adenocarcinoma)", "1.374", "0.802", "2.352", "0.247"], ["SPINK4 expression", "(high vs. low)", "0.479", "0.321", "0.714", "0.000"], ["Multivariate analysis", "", "", "", "", ""], ["Age", "(per year)", "1.040", "1.003", "1.078", "0.034"], ["TNM stage", "(III-IV vs. I-II)", "3.750", "1.323", "10.635", "0.013"], ["Perineural invasion", "(yes vs. No)", "2.359", "0.864", "6.445", "0.094"], ["Venous invasion", "(yes vs. No)", "2.773", "1.066", "7.217", "0.037"], ["SPINK4 expression", "(high vs. low)", "0.301", "0.116", "0.785", "0.014"]], "row_count": 41, "column_count": 7, "numeric_cells": 140, "header_rows": 1, "locator": "section[14]/table-wrap[2]#Tab3"}}, {"id": "asset:table:pmid:31888570:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:72988ef52ab9e9134a777211301acf324fd78449d78d096dc0df11fd8c81538a", "bytes": 2578, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[3]#Tab4", "version": null, "note": "Multivariate analysis of indicators for survival in CRC patients in in our own cohort", "structure": {"pmcid": "PMC6938003", "section_index": 14, "section_title": "Correlations between SPINK4 expression and CRC patient survival", "row_count": 38, "column_count": 6}, "table": {"label": "Table 4", "caption": "Multivariate analysis of indicators for survival in CRC patients in in our own cohort", "rows": [["Variable", "Group", "HR", "(95% CI)", "", "P value"], ["Overall survival"], ["Univariate analysis"], ["Gender", "(female vs. male)", "0.583", "0.275", "1.236", "0.159"], ["Age", "(per year)", "1.037", "1.004", "1.070", "0.026"], ["BMI", "(per kg/m2)", "0.963", "0.862", "1.074", "0.496"], ["TNM stage", "(per stage)", "3.135", "1.936", "5.078", "0.000"], ["Tumor size", "(per cm)", "1.091", "0.925", "1.287", "0.300"], ["Pretreatment CEA level", "(per ng/mL)", "1.014", "1.002", "1.027", "0.024"], ["Pretreatment CA199 level", "(per U/ml)", "1.004", "1.001", "1.007", "0.004"], ["Histological type", "(mucinous adenocarcinoma vs. adenocarcinoma)", "1.994", "0.693", "5.739", "0.201"], ["Perineural invasion", "(yes vs. No)", "3.796", "1.133", "12.712", "0.031"], ["Venus invasion", "(yes vs. No)", "1.398", "0.533", "3.669", "0.496"], ["Tumor location", "", "0.981", "0.568", "1.696", "0.946"], ["Differentiation", "(well to moderately differentiated vs. poorly differentiated)", "1.435", "0.341", "6.043", "0.622"], ["SPINK4 expression", "(high vs. low)", "0.289", "0.100", "0.832", "0.021"], ["Multivariate analysis"], ["Age", "(per year)", "1.034", "1.003", "1.066", "0.031"], ["TNM stage", "(per stage)", "3.093", "1.873", "5.109", "0.000"], ["SPINK4 expression", "(high vs. low)", "0.299", "0.103", "0.872", "0.027"], ["Disease-free survival"], ["Univariate analysis"], ["Gender", "(female vs. male)", "0.616", "0.298", "1.273", "0.191"], ["Age", "(per year)", "1.034", "1.003", "1.066", "0.033"], ["BMI", "(per kg/m2)", "0.962", "0.867", "1.069", "0.474"], ["TNM stage", "(per stage)", "3.104", "1.943", "4.957", "0.000"], ["Tumor size", "(per cm)", "1.099", "0.936", "1.291", "0.247"], ["Pretreatment CEA level", "(per ng/mL)", "1.012", "1.000", "1.024", "0.059"], ["Pretreatment CA199 level", "(per U/ml)", "1.004", "1.001", "1.007", "0.003"], ["Histological type", "(mucinous adenocarcinoma vs. adenocarcinoma)", "1.916", "0.670", "5.482", "0.225"], ["Perineural invasion", "(yes vs. No)", "2.918", "0.873", "9.757", "0.082"], ["Venus invasion", "(yes vs. No)", "1.534", "0.629", "3.741", "0.347"], ["Tumor location", "", "1.051", "0.617", "1.792", "0.855"], ["Differentiation", "(well to moderately differentiated vs. poorly differentiated)", "1.424", "0.340", "5.975", "0.629"], ["SPINK4 expression", "(high vs. low)", "0.261", "0.091", "0.747", "0.012"], ["Multivariate analysis"], ["TNM stage", "(per stage)", "3.298", "1.986", "5.475", "0.000"], ["SPINK4 expression", "(high vs. low)", "0.264", "0.091", "0.766", "0.014"]], "row_count": 38, "column_count": 6, "numeric_cells": 127, "header_rows": 1, "locator": "section[14]/table-wrap[3]#Tab4"}}], "gaps": ["asset:data:geo:GSE24551 not downloaded", "asset:data:geo:GSE24551 licence not read", "asset:data:geo:GSE32323 not downloaded", "asset:data:geo:GSE32323 licence not read", "asset:data:geo:GSE3880 not downloaded", "asset:data:geo:GSE3880 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE81861 not downloaded", "asset:data:geo:GSE81861 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "dividual hazard ratios (HRs) for the survival rate"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox proportional hazards"}}, {"id": "method-3", "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": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 0.8, "band": "high", "quote": "χ2"}}], "targets": [], "gaps": []}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE24551", "GSE39582", "GSE32323", "GSE3880", "GSE81861"], "resolved_accessions": ["GSE24551", "GSE39582", "GSE32323", "GSE3880", "GSE81861"], "statements": ["The dataset supporting the conclusions of this article is included within the article and its Additional file 3: Table S1. All TCGA related data can be obtained from the TCGA Data Portal via https://tcga-data.nci.nih.gov/. All GEO related data can be obtained from the GEO Data Portal via https://www.ncbi.nlm.nih.gov/geo/."], "basis": "The paper names GSE24551, GSE39582, GSE32323, GSE3880, GSE81861 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:31888570", "data:geo:GSE24551", "asset:table:pmid:31888570:1", "asset:table:pmid:31888570:2", "asset:table:pmid:31888570:3", "asset:table:pmid:31888570:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE24551"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:54:28Z", "independence": "single_reader"}, "evidence_check": {"method": null, "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34714, "completion_tokens": 2740, "cached_tokens": 784}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:31888570", "type": "paper", "label": "pmid:31888570"}, {"id": "source:pmid:31888570", "type": "manuscript", "label": "PMID 31888570 full text"}, {"id": "data:geo:GSE24551", "type": "dataset", "label": "GEO GSE24551"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31888570", "type": "paper", "label": "pmid:31888570"}, {"id": "source:pmid:31888570", "type": "manuscript", "label": "PMID 31888570 full text"}, {"id": "data:geo:GSE24551", "type": "dataset", "label": "GEO GSE24551"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31888570", "type": "extraction", "used": ["source:pmid:31888570"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE24551", "type": "accession_resolution", "used": ["data:geo:GSE24551"], "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:31888570", "parent_hash": "sha256:fdba3a903c31a9a17e74399c36ff8093dcef8c477f1e4b50d780986246e4bd48", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE24551 licence not read", "asset:data:geo:GSE24551 not downloaded", "asset:data:geo:GSE32323 licence not read", "asset:data:geo:GSE32323 not downloaded", "asset:data:geo:GSE3880 licence not read", "asset:data:geo:GSE3880 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "asset:data:geo:GSE81861 licence not read", "asset:data:geo:GSE81861 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ata mining in the Human Protein Atlas and by immunohistochemical staining of samples from 81 CRC cases in our", "es were retrospectively collected to perform IHC staining. All patients had received radical", "9%, P<0.001, Fig. 6c). At the protein level, IHC staining was carried out in our own cohort,"], "order_basis": "paper_text_order:698", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["etastasis, proliferation, EMT, angiogenesis, apoptosis, cell cycle, differentiation, DNA damage, DN"], "order_basis": "paper_text_order:3582", "id": "assay:2"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Kaplan-Meier"], "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":"2026-11-04T00:46:18+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}}}