Identification and Experimental Validation of Oxidative Stress-Related Biomarkers in Ulcerative Colitis Using Machine Learning.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:40860945", "kind": "science-record", "revision": 3, "content_hash": "sha256:8e5f539ed6f7fd2b0aa0e963288c69ace54e39557fe56e1000f8892f44a50324", "created_at": "2026-11-01T20:30:59Z", "updated_at": "2026-11-01T22:14:38Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and Experimental Validation of Oxidative Stress-Related Biomarkers in Ulcerative Colitis Using Machine Learning.", "doi": "10.2147/JIR.S520874", "pmid": "40860945", "authors": ["Siwei Duan", "Qincheng Yi", "Min Qiu", "Zeming Zhu", "Ziyi Zhang", "Yong Gao", "Dong Zhang"], "journal": "Journal of inflammation research", "year": 2025, "abstract": "Purpose: Ulcerative colitis (UC) remains challenging to diagnose and treat due to a lack of reliable biomarkers. This study investigates oxidative stress-related targets in UC using bioinformatics and experimental validation.\nMethods: We analyzed four GEO datasets and oxidative-stress genes from MSigDB, applying differential analysis, LASSO regression (for feature selection), and random forest (for robust biomarker identification). An artificial neural network (ANN) diagnostic model was constructed, followed by chromosomal distribution analysis, immune infiltration assessment, and drug screening. Hub gene expression was validated in a 3% DSS-induced colitis mouse model via qPCR and Western blot.\nResults: Ultimately there were 6 hub genes identified: DUOX2, ETFDH, GPX8, ITGA5, NPY, and PDK2, which were validated with 3 other datasets. In the DSS-colitis model, DUOX2 and ITGA5 were significantly upregulated (p < 0.05), whereas ETFDH, PDK2, and NPY were downregulated. GPX8 protein expression was elevated in colonic mucosa compared to controls. These findings were further validated in three independent datasets (GSE48958, GSE16879, GSE36807).\nConclusion: Our study identifies six oxidative stress-related biomarkers in UC using machine learning and experimental validation. These findings provide potential diagnostic and therapeutic targets for UC management, paving the way for further clinical investigations.", "claims": [{"id": "claim-method", "statement": "We analyzed four GEO datasets and oxidative-stress genes from MSigDB, applying differential analysis, LASSO regression (for feature selection), and random forest (for robust biomarker identification).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40860945", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We analyzed four GEO datasets and oxidative-stress genes from MSigDB, applying differential analysis, LASSO regression (for feature selection), and random forest (for robust biomarker identification)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:40860945", "locator": "sections[32] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Ultimately there were 6 hub genes identified: DUOX2, ETFDH, GPX8, ITGA5, NPY, and PDK2, which were validated with 3 other datasets.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:40860945", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Ultimately there were 6 hub genes identified: DUOX2, ETFDH, GPX8, ITGA5, NPY, and PDK2, which were validated with 3 other datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Ultimately there were 6 hub genes identified: DUOX2, ETFDH, GPX8, ITGA5, NPY, and PDK2, which were validated with 3 other datasets.", "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:40860945"], "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:GSE16879"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:machine_learning_random_forest", "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:GSE16879"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:machine_learning_random_forest"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:40860945", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/JIR.S520874", "sha256": "sha256:9e5979072b2225db176f94ddc1ebabac038f15213d9f60dceec11fb2553322b3", "bytes": 64190, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/JIR.S520874", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12375314", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16879", "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=GSE16879", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16879", "version": null, "note": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM364627", "GSM364628", "GSM364629", "GSM364630", "GSM364631", "GSM364632", "GSM364633", "GSM364634", "GSM364635", "GSM364636", "GSM364637", "GSM364638", "GSM364639", "GSM364640", "GSM364641", "GSM364642", "GSM364643", "GSM364644", "GSM364645", "GSM364646", "GSM364647", "GSM364648", "GSM364649", "GSM364650", "GSM364651", "GSM364652", "GSM364653", "GSM364654", "GSM364655", "GSM364656", "GSM422963", "GSM422965", "GSM422967", "GSM422969", "GSM422971", "GSM422973", "GSM422975", "GSM422977", "GSM422979", "GSM422981", "GSM422983", "GSM422985", "GSM422987", "GSM422989", "GSM422991", "GSM422993", "GSM422995", "GSM422997", "GSM422999", "GSM423001", "GSM423003", "GSM423005", "GSM423007", "GSM423009", "GSM423010", "GSM423011", "GSM423012", "GSM423013", "GSM423014", "GSM423015", "GSM423016", "GSM423017", "GSM423018", "GSM423019", "GSM423020", "GSM423021", "GSM423022", "GSM423023", "GSM423024", "GSM423025", "GSM423026", "GSM423027", "GSM423028", "GSM423029", "GSM423030", "GSM423031", "GSM423032", "GSM423033", "GSM423034", "GSM423035", "GSM423036", "GSM423037", "GSM423038", "GSM423039", "GSM423040", "GSM423041", "GSM423042", "GSM423043", "GSM423044", "GSM423045", "GSM423046", "GSM423047", "GSM423048", "GSM423049", "GSM423050", "GSM423051", "GSM423052", "GSM423053", "GSM423054", "GSM423055", "GSM423056", "GSM423057", "GSM423058", "GSM423059", "GSM423060", "GSM423061", "GSM423062", "GSM423063", "GSM423064", "GSM423065", "GSM423066", "GSM423067", "GSM423068", "GSM423069", "GSM423070", "GSM423071", "GSM423072", "GSM423073", "GSM423074", "GSM423075", "GSM423076", "GSM423077", "GSM423078", "GSM423079", "GSM423080", "GSM423081", "GSM423082", "GSM423083", "GSM423084", "GSM423085", "GSM423086", "GSM423087", "GSM423088"], "sample_count": 133, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Mucosal expression profiling in patients with inflammatory bowel disease before and after first infliximab treatment", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE36807", "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=GSE36807", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE36807", "version": null, "note": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM901319", "GSM901320", "GSM901321", "GSM901322", "GSM901323", "GSM901324", "GSM901325", "GSM901326", "GSM901327", "GSM901328", "GSM901329", "GSM901330", "GSM901331", "GSM901332", "GSM901333", "GSM901334", "GSM901335", "GSM901336", "GSM901337", "GSM901338", "GSM901339", "GSM901340", "GSM901341", "GSM901342", "GSM901343", "GSM901344", "GSM901345", "GSM901346", "GSM901347", "GSM901348", "GSM901349", "GSM901350", "GSM901351", "GSM901352", "GSM901353"], "sample_count": 35, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Genome-wide analysis of Crohn's disease and ulcerative colitis biopsy samples.", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE38713", "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=GSE38713", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38713", "version": null, "note": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM948550", "GSM948551", "GSM948552", "GSM948553", "GSM948554", "GSM948555", "GSM948556", "GSM948557", "GSM948558", "GSM948559", "GSM948560", "GSM948561", "GSM948562", "GSM948563", "GSM948564", "GSM948565", "GSM948566", "GSM948567", "GSM948568", "GSM948569", "GSM948570", "GSM948571", "GSM948572", "GSM948573", "GSM948574", "GSM948575", "GSM948576", "GSM948577", "GSM948578", "GSM948579", "GSM948580", "GSM948581", "GSM948582", "GSM948583", "GSM948584", "GSM948585", "GSM948586", "GSM948587", "GSM948588", "GSM948589", "GSM948590", "GSM948591", "GSM948592"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from intestinal mucosa of patients with UC", "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:GSE48958", "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=GSE48958", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE48958", "version": null, "note": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1187602", "GSM1187603", "GSM1187604", "GSM1187605", "GSM1187606", "GSM1187607", "GSM1187608", "GSM1187609", "GSM1187610", "GSM1187611", "GSM1187612", "GSM1187613", "GSM1187614", "GSM1187615", "GSM1187616", "GSM1187617", "GSM1187618", "GSM1187619", "GSM1187620", "GSM1187621", "GSM1187622"], "sample_count": 21, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Mucosal gene expression profiling in (un)inflamed colon of patients with ulcerative colitis (UC)", "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:GSE59071", "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=GSE59071", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE59071", "version": null, "note": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1426071", "GSM1426072", "GSM1426073", "GSM1426074", "GSM1426075", "GSM1426076", "GSM1426077", "GSM1426078", "GSM1426079", "GSM1426080", "GSM1426081", "GSM1426082", "GSM1426083", "GSM1426084", "GSM1426085", "GSM1426086", "GSM1426087", "GSM1426088", "GSM1426089", "GSM1426090", "GSM1426091", "GSM1426092", "GSM1426093", "GSM1426094", "GSM1426095", "GSM1426096", "GSM1426097", "GSM1426098", "GSM1426099", "GSM1426100", "GSM1426101", "GSM1426102", "GSM1426103", "GSM1426104", "GSM1426105", "GSM1426106", "GSM1426107", "GSM1426108", "GSM1426109", "GSM1426110", "GSM1426111", "GSM1426112", "GSM1426113", "GSM1426114", "GSM1426115", "GSM1426116", "GSM1426117", "GSM1426118", "GSM1426119", "GSM1426120", "GSM1426121", "GSM1426122", "GSM1426123", "GSM1426124", "GSM1426125", "GSM1426126", "GSM1426127", "GSM1426128", "GSM1426129", "GSM1426130", "GSM1426131", "GSM1426132", "GSM1426133", "GSM1426134", "GSM1426135", "GSM1426136", "GSM1426137", "GSM1426138", "GSM1426139", "GSM1426140", "GSM1426141", "GSM1426142", "GSM1426143", "GSM1426144", "GSM1426145", "GSM1426146", "GSM1426147", "GSM1426148", "GSM1426149", "GSM1426150", "GSM1426151", "GSM1426152", "GSM1426153", "GSM1426154", "GSM1426155", "GSM1426156", "GSM1426157", "GSM1426158", "GSM1426159", "GSM1426160", "GSM1426161", "GSM1426162", "GSM1426163", "GSM1426164", "GSM1426165", "GSM1426166", "GSM1426167", "GSM1426168", "GSM1426169", "GSM1426170", "GSM1426171", "GSM1426172", "GSM1426173", "GSM1426174", "GSM1426175", "GSM1426176", "GSM1426177", "GSM1426178", "GSM1426179", "GSM1426180", "GSM1426181", "GSM1426182", "GSM1426183", "GSM1426184", "GSM1426185", "GSM1426186"], "sample_count": 116, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Mucosal gene expression profiling in patients with inflammatory bowel disease", "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:GSE87465", "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=GSE87465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87465", "version": null, "note": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2332079", "GSM2332080", "GSM2332081", "GSM2332082", "GSM2332083", "GSM2332084", "GSM2332085", "GSM2332086", "GSM2332087", "GSM2332088", "GSM2332089", "GSM2332090", "GSM2332091", "GSM2332092", "GSM2332093", "GSM2332094", "GSM2332095", "GSM2332096", "GSM2332097"], "sample_count": 19, "group_sizes": null, "group_sizes_basis": null, "platform": "13158", "taxon": "Homo sapiens", "title": "Gene expression profiling of mucosal biopsies from pediatric patients with moderately to severely active ulcerative colitis", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE87466", "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=GSE87466", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE87466", "version": null, "note": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2332098", "GSM2332099", "GSM2332100", "GSM2332101", "GSM2332102", "GSM2332103", "GSM2332104", "GSM2332105", "GSM2332106", "GSM2332107", "GSM2332108", "GSM2332109", "GSM2332110", "GSM2332111", "GSM2332112", "GSM2332113", "GSM2332114", "GSM2332115", "GSM2332116", "GSM2332117", "GSM2332118", "GSM2332119", "GSM2332120", "GSM2332121", "GSM2332122", "GSM2332123", "GSM2332124", "GSM2332125", "GSM2332126", "GSM2332127", "GSM2332128", "GSM2332129", "GSM2332130", "GSM2332131", "GSM2332132", "GSM2332133", "GSM2332134", "GSM2332135", "GSM2332136", "GSM2332137", "GSM2332138", "GSM2332139", "GSM2332140", "GSM2332141", "GSM2332142", "GSM2332143", "GSM2332144", "GSM2332145", "GSM2332146", "GSM2332147", "GSM2332148", "GSM2332149", "GSM2332150", "GSM2332151", "GSM2332152", "GSM2332153", "GSM2332154", "GSM2332155", "GSM2332156", "GSM2332157", "GSM2332158", "GSM2332159", "GSM2332160", "GSM2332161", "GSM2332162", "GSM2332163", "GSM2332164", "GSM2332165", "GSM2332166", "GSM2332167", "GSM2332168", "GSM2332169", "GSM2332170", "GSM2332171", "GSM2332172", "GSM2332173", "GSM2332174", "GSM2332175", "GSM2332176", "GSM2332177", "GSM2332178", "GSM2332179", "GSM2332180", "GSM2332181", "GSM2332182", "GSM2332183", "GSM2332184", "GSM2332185", "GSM2332186", "GSM2332187", "GSM2332188", "GSM2332189", "GSM2332190", "GSM2332191", "GSM2332192", "GSM2332193", "GSM2332194", "GSM2332195", "GSM2332196", "GSM2332197", "GSM2332198", "GSM2332199", "GSM2332200", "GSM2332201", "GSM2332202", "GSM2332203", "GSM2332204", "GSM2332205"], "sample_count": 108, "group_sizes": null, "group_sizes_basis": null, "platform": "13158", "taxon": "Homo sapiens", "title": "Gene expression profiling of mucosal biopsies from adult patients with moderately to severely active ulcerative colitis", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE16879 not downloaded", "asset:data:geo:GSE16879 licence not read", "asset:data:geo:GSE36807 not downloaded", "asset:data:geo:GSE36807 licence not read", "asset:data:geo:GSE38713 not downloaded", "asset:data:geo:GSE38713 licence not read", "asset:data:geo:GSE48958 not downloaded", "asset:data:geo:GSE48958 licence not read", "asset:data:geo:GSE59071 not downloaded", "asset:data:geo:GSE59071 licence not read", "asset:data:geo:GSE87465 not downloaded", "asset:data:geo:GSE87465 licence not read", "asset:data:geo:GSE87466 not downloaded", "asset:data:geo:GSE87466 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We analyzed four GEO datasets and oxidative-stress genes from MSigDB, applying differential analysis, LASSO regression (for feature selection), and random forest (for robust biomarker identification)."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor", "method.machine_learning_random_forest"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["machine_learning_random_forest"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: random_forest."}, "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": ["GSE38713", "GSE59071", "GSE87465", "GSE87466", "GSE48958", "GSE16879", "GSE36807"], "resolved_accessions": ["GSE38713", "GSE59071", "GSE87465", "GSE87466", "GSE48958", "GSE16879", "GSE36807"], "statements": ["The datasets used in this study can be accessed through the GEO database (https://www.ncbi.nlm.nih.gov/geo/). All raw data and code are available from the corresponding author Dong Zhang,with a reasonable request."], "basis": "The paper names GSE38713, GSE59071, GSE87465, GSE87466, GSE48958, GSE16879, GSE36807 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40860945", "data:geo:GSE16879"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "machine_learning_random_forest", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16879"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:00:37Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 17464, "completion_tokens": 1647, "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:40860945", "type": "paper", "label": "pmid:40860945"}, {"id": "source:pmid:40860945", "type": "manuscript", "label": "PMID 40860945 full text"}, {"id": "data:geo:GSE16879", "type": "dataset", "label": "GEO GSE16879"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:40860945", "type": "paper", "label": "pmid:40860945"}, {"id": "source:pmid:40860945", "type": "manuscript", "label": "PMID 40860945 full text"}, {"id": "data:geo:GSE16879", "type": "dataset", "label": "GEO GSE16879"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-40860945", "type": "extraction", "used": ["source:pmid:40860945"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16879", "type": "accession_resolution", "used": ["data:geo:GSE16879"], "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:40860945", "parent_hash": "sha256:3566d34a2ebbe01e41db9b51799bf5c98ad4eb04185879746af4b8f986d11eef", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE16879 licence not read", "asset:data:geo:GSE16879 not downloaded", "asset:data:geo:GSE36807 licence not read", "asset:data:geo:GSE36807 not downloaded", "asset:data:geo:GSE38713 licence not read", "asset:data:geo:GSE38713 not downloaded", "asset:data:geo:GSE48958 licence not read", "asset:data:geo:GSE48958 not downloaded", "asset:data:geo:GSE59071 licence not read", "asset:data:geo:GSE59071 not downloaded", "asset:data:geo:GSE87465 licence not read", "asset:data:geo:GSE87465 not downloaded", "asset:data:geo:GSE87466 licence not read", "asset:data:geo:GSE87466 not downloaded", "execution.not_run", "method.machine_learning_random_forest", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:machine_learning_random_forest"], "assays": [{"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["on was validated in a 3% DSS-induced colitis mouse model via qPCR and Western blot. Results: Ultimate", "on was validated in a 3% DSS-induced colitis mouse model via qPCR and Western blot. Results: Ul", "e: SCXK (Guangdong) 002020–0051; China). The mice were housed in six cages (3–4 mice per cage) sett", "rimental Validation Three groups of C57BL/6J mice were randomly assigned to a control group, a 3% D"], "order_basis": "paper_text_order:749", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["in a 3% DSS-induced colitis mouse model via qPCR and Western blot. Results: Ultimately there", "length in each group of mice (Unit: cm). (g) qPCR validation of hub genes. (h) Western blot va"], "order_basis": "paper_text_order:766", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["DSS-induced colitis mouse model via qPCR and Western blot. Results: Ultimately there were 6 hub genes", ": cm). (g) qPCR validation of hub genes. (h) Western blot validation of hub genes. (In Figures d,e and"], "order_basis": "paper_text_order:774", "id": "assay:3"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We analyzed four GEO datasets and oxidative-stress genes from MSigDB, applying differential analysis, LASSO regression (for feature selection), and random forest (for robust biomarker identification)."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}