Identification of Pathologic and Prognostic Genes in Prostate Cancer Based on Database Mining.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35360870", "kind": "science-record", "revision": 4, "content_hash": "sha256:93191a0c4a4b297b07df9034e8ace1d88c09e190803720bcd79af4aea21478e9", "created_at": "2026-11-01T18:14:10Z", "updated_at": "2026-11-01T22:06:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Pathologic and Prognostic Genes in Prostate Cancer Based on Database Mining.", "doi": "10.3389/fgene.2022.854531", "pmid": "35360870", "authors": ["Kun Liu", "Yijun Chen", "Pengmian Feng", "Yucheng Wang", "Mengdi Sun", "Tao Song", "Jun Tan", "Chunyang Li", "Songpo Liu", "Qinghong Kong", "Jidong Zhang"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Background: Prostate cancer (PCa) is an epithelial malignant tumor that occurs in the urinary system with high incidence and is the second most common cancer among men in the world. Thus, it is important to screen out potential key biomarkers for the pathogenesis and prognosis of PCa. The present study aimed to identify potential biomarkers to reveal the underlying molecular mechanisms. Methods: Differentially expressed genes (DEGs) between PCa tissues and matched normal tissues from The Cancer Genome Atlas Prostate Adenocarcinoma (TCGA-PRAD) dataset were screened out by R software. Weighted gene co-expression network analysis was performed primarily to identify statistically significant genes for clinical manifestations. Protein-protein interaction (PPI) network analysis and network screening were performed based on the STRING database in conjunction with Cytoscape software. Hub genes were then screened out by Cytoscape in conjunction with stepwise algorithm and multivariate Cox regression analysis to construct a risk model. Gene expression in different clinical manifestations and survival analysis correlated with the expression of hub genes were performed. Moreover, the protein expression of hub genes was validated by the Human Protein Atlas database. Results: A total of 1,621 DEGs (870 downregulated genes and 751 upregulated genes) were identified from the TCGA-PRAD dataset. Eight prognostic genes [BUB1, KIF2C, CCNA2, CDC20, CCNB2, PBK, RRM2, and CDC45] and four hub genes (BUB1, KIF2C, CDC20, and PBK) potentially correlated with the pathogenesis of PCa were identified. A prognostic model with good predictive power for survival was constructed and was validated by the dataset in GSE21032. The survival analysis demonstrated that the expression of RRM2 was statistically significant to the prognosis of PCa, indicating that RRM2 may potentially play an important role in the PCa progression. Conclusion: The present study implied that RRM2 was associated with prognosis and could be used as a potential therapeutic target for PCa clinical treatment.", "claims": [{"id": "claim-method", "statement": "In our study, the key genes associated with overall survival (OS) were screened out from the top 25 candidate hub genes by Cox proportional hazard regression analysis based on the TCGA dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35360870", "locator": "sections[9] \"Hub Gene Mining and Construction of a Prognostic Risk Model\" paragraph 2", "quote": "In our study, the key genes associated with overall survival (OS) were screened out from the top 25 candidate hub genes by Cox proportional hazard regression analysis based on the TCGA dataset."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35360870", "locator": "sections[21] \"Data Availability Statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study constructed an eight-gene prognostic risk model for prostate cancer and found that high RRM2 expression was associated with poor prognosis.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "We found that RRM2 was statistically significant to the prognosis of prostate cancer patients (p < 0.05) (Figure 12A)."}, "evidence": [{"asset": "source:pmid:35360870", "locator": "sections[18] \"RRM2 Might Be a Potential Biomarker for PCa Prognosis\" paragraph 2", "quote": "We found that RRM2 was statistically significant to the prognosis of prostate cancer patients (p < 0.05) (Figure 12A)."}, {"asset": "source:pmid:35360870", "locator": "sections[18] \"RRM2 Might Be a Potential Biomarker for PCa Prognosis\" paragraph 2", "quote": "All results revealed that the high expression of RRM2 led to poor prognosis, indicating that RRM2 may be an independent potential biomarker of PCa prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study constructed an eight-gene prognostic risk model for prostate cancer and found that high RRM2 expression was associated with poor prognosis.", "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:35360870"], "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:GSE21032"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE21032"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35360870", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2022.854531", "sha256": "sha256:6d23d78216bfe9cf88ea4fcba87090fb4dc2c444994d29504fcef29a06c2a28e", "bytes": 36119, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2022.854531", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8963346", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21032", "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=GSE21032", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21032", "version": null, "note": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM525575", "GSM525576", "GSM525577", "GSM525578", "GSM525579", "GSM525580", "GSM525581", "GSM525582", "GSM525583", "GSM525584", "GSM525585", "GSM525586", "GSM525587", "GSM525588", "GSM525589", "GSM525590", "GSM525591", "GSM525592", "GSM525593", "GSM525594", "GSM525595", "GSM525596", "GSM525597", "GSM525598", "GSM525599", "GSM525600", "GSM525601", "GSM525602", "GSM525603", "GSM525604", "GSM525605", "GSM525606", "GSM525607", "GSM525608", "GSM525609", "GSM525610", "GSM525611", "GSM525612", "GSM525613", "GSM525614", "GSM525615", "GSM525616", "GSM525617", "GSM525618", "GSM525619", "GSM525620", "GSM525621", "GSM525622", "GSM525623", "GSM525624", "GSM525625", "GSM525626", "GSM525627", "GSM525628", "GSM525629", "GSM525630", "GSM525631", "GSM525632", "GSM525633", "GSM525634", "GSM525635", "GSM525636", "GSM525637", "GSM525638", "GSM525639", "GSM525640", "GSM525641", "GSM525642", "GSM525643", "GSM525644", "GSM525645", "GSM525646", "GSM525647", "GSM525648", "GSM525649", "GSM525650", "GSM525651", "GSM525652", "GSM525653", "GSM525654", "GSM525655", "GSM525656", "GSM525657", "GSM525658", "GSM525659", "GSM525660", "GSM525661", "GSM525662", "GSM525663", "GSM525664", "GSM525665", "GSM525666", "GSM525667", "GSM525668", "GSM525669", "GSM525670", "GSM525671", "GSM525672", "GSM525673", "GSM525674", "GSM525675", "GSM525676", "GSM525677", "GSM525678", "GSM525679", "GSM525680", "GSM525681", "GSM525682", "GSM525683", "GSM525684", "GSM525685", "GSM525686", "GSM525687", "GSM525688", "GSM525689", "GSM525690", "GSM525691", "GSM525692", "GSM525693", "GSM525694", "GSM525695", "GSM525696", "GSM525697", "GSM525698", "GSM525699", "GSM525700", "GSM525701", "GSM525702", "GSM525703", "GSM525704", "GSM525705", "GSM525706", "GSM525707", "GSM525708", "GSM525709", "GSM525710", "GSM525711", "GSM525712", "GSM525713", "GSM525714", "GSM525715", "GSM525716", "GSM525717", "GSM525718", "GSM525719", "GSM525720", "GSM525721", "GSM525722", "GSM525723", "GSM525724", "GSM525725", "GSM525726", "GSM525727", "GSM525728", "GSM525729", "GSM525730", "GSM525731", "GSM525732", "GSM525733", "GSM525734", "GSM525735", "GSM525736", "GSM525737", "GSM525738", "GSM525739", "GSM525740", "GSM525741", "GSM525742", "GSM525743", "GSM525744", "GSM525745", "GSM525746", "GSM525747", "GSM525748", "GSM525749", "GSM525750", "GSM525751", "GSM525752", "GSM525753", "GSM525754", "GSM525755", "GSM525756", "GSM525757", "GSM525758", "GSM525759", "GSM525760", "GSM525761", "GSM525762", "GSM525763", "GSM525764", "GSM525765", "GSM525766", "GSM525767", "GSM525768", "GSM525769", "GSM525770", "GSM525771", "GSM525772", "GSM525773", "GSM525774", "GSM525775", "GSM525776", "GSM525777", "GSM525778", "GSM525779", "GSM525780", "GSM525781", "GSM525782", "GSM525783", "GSM525784", "GSM525785", "GSM525786", "GSM525787", "GSM525788", "GSM525789", "GSM525790", "GSM525791", "GSM525792", "GSM525793", "GSM525794", "GSM525795", "GSM525796", "GSM525797", "GSM525798", "GSM525799", "GSM525800", "GSM525801", "GSM525802", "GSM525803", "GSM525804", "GSM525805", "GSM526134", "GSM526135", "GSM526136", "GSM526137", "GSM526138", "GSM526139", "GSM526140", "GSM526141", "GSM526142", "GSM526143", "GSM526144", "GSM526145", "GSM526146", "GSM526147", "GSM526148", "GSM526149", "GSM526150", "GSM526151", "GSM526152", "GSM526153", "GSM526154", "GSM526155", "GSM526156", "GSM526157", "GSM526158", "GSM526159", "GSM526160", "GSM526161", "GSM526162", "GSM526163", "GSM526164", "GSM526165", "GSM526166", "GSM526167", "GSM526168", "GSM526169", "GSM526170", "GSM526171", "GSM526172", "GSM526173", "GSM526174", "GSM526175", "GSM526176", "GSM526177", "GSM526178", "GSM526179", "GSM526180", "GSM526181", "GSM526182", "GSM526183", "GSM526184", "GSM526185", "GSM526186", "GSM526187", "GSM526188", "GSM526189", "GSM526190", "GSM526191", "GSM526192", "GSM526193", "GSM526194", "GSM526195", "GSM526196", "GSM526197", "GSM526198", "GSM526199", "GSM526200", "GSM526201", "GSM526202", "GSM526203", "GSM526204", "GSM526205", "GSM526206", "GSM526207", "GSM526208", "GSM526209", "GSM526210", "GSM526211", "GSM526212", "GSM526213", "GSM526214", "GSM526215", "GSM526216", "GSM526217", "GSM526218", "GSM526219", "GSM526220", "GSM526221", "GSM526222", "GSM526223", "GSM526224", "GSM526225", "GSM526226", "GSM526227", "GSM526228", "GSM526229", "GSM526230", "GSM526231", "GSM526232", "GSM526233", "GSM526234", "GSM526235", "GSM526236", "GSM526237", "GSM526238", "GSM526239", "GSM526240", "GSM526241", "GSM526242", "GSM526243", "GSM526244", "GSM526245", "GSM526246", "GSM526247", "GSM526248", "GSM526249", "GSM526250", "GSM526251", "GSM526252", "GSM526253", "GSM526254", "GSM526255", "GSM526256", "GSM526257", "GSM526258", "GSM526259", "GSM526260", "GSM526261", "GSM526262", "GSM526263", "GSM526264", "GSM526265", "GSM526266", "GSM526267", "GSM526268", "GSM526269", "GSM526270", "GSM526271", "GSM526272", "GSM526273", "GSM526274", "GSM526275", "GSM526276", "GSM526277", "GSM526278", "GSM526279", "GSM526280", "GSM526281", "GSM526282", "GSM526283", "GSM526284", "GSM526285", "GSM526286", "GSM526287", "GSM526288", "GSM526289", "GSM526290", "GSM526291", "GSM526292", "GSM526293", "GSM526294", "GSM526295", "GSM526296", "GSM526297", "GSM526298", "GSM526299", "GSM526300", "GSM526301", "GSM526302", "GSM526303", "GSM526304", "GSM526305", "GSM526306", "GSM526307", "GSM526308", "GSM526309", "GSM526310", "GSM526311", "GSM526312", "GSM526313", "GSM526314", "GSM526315", "GSM526316", "GSM526317", "GSM526318", "GSM526419", "GSM526420", "GSM526421", "GSM526422", "GSM526423", "GSM526424", "GSM526425", "GSM526426", "GSM526427", "GSM526428", "GSM526429", "GSM526430", "GSM526431", "GSM526432", "GSM526433", "GSM526434", "GSM526435", "GSM526436", "GSM526437", "GSM526438", "GSM526439", "GSM526440", "GSM526441", "GSM526442", "GSM526443", "GSM526444", "GSM526445", "GSM526446", "GSM526447", "GSM526448", "GSM526449", "GSM526450", "GSM526451", "GSM526452", "GSM526453", "GSM526454", "GSM526455", "GSM526456", "GSM526457", "GSM526458", "GSM526459", "GSM526460", "GSM526461", "GSM526462", "GSM526463", "GSM526464", "GSM526465", "GSM526466", "GSM526467", "GSM526468", "GSM526469", "GSM526470", "GSM526471", "GSM526472", "GSM526473", "GSM526474", "GSM526475", "GSM526476", "GSM526477", "GSM526478", "GSM526479", "GSM526480", "GSM526481", "GSM526482", "GSM526483", "GSM526484", "GSM526485", "GSM526486", "GSM526487", "GSM526488", "GSM526489", "GSM526490", "GSM526491", "GSM526492", "GSM526493", "GSM526494", "GSM526495", "GSM526496", "GSM526497", "GSM526498", "GSM526499", "GSM526500", "GSM526501", "GSM526502", "GSM526503", "GSM526504", "GSM526505", "GSM526506", "GSM526507", "GSM526508", "GSM526509", "GSM526510", "GSM526511", "GSM526512", "GSM526513", "GSM526514", "GSM526515", "GSM526516", "GSM526517", "GSM526518", "GSM526519", "GSM526520", "GSM526521", "GSM526522", "GSM526523", "GSM526524", "GSM526525", "GSM526526", "GSM526527", "GSM526528", "GSM526529", "GSM526530", "GSM526531", "GSM526532", "GSM526533", "GSM526534", "GSM526535", "GSM526536", "GSM526537", "GSM526538", "GSM526539", "GSM526540", "GSM526541", "GSM526542", "GSM526543", "GSM526544", "GSM526545", "GSM526546", "GSM526547", "GSM526548", "GSM526549", "GSM526550", "GSM526551", "GSM526552", "GSM526553", "GSM526554", "GSM526555", "GSM526556", "GSM526557", "GSM526558", "GSM526559", "GSM526560", "GSM527858", "GSM527859", "GSM527860", "GSM527861", "GSM527862", "GSM527863", "GSM527864", "GSM527865", "GSM527866", "GSM527867", "GSM527868", "GSM527869", "GSM527870", "GSM527871", "GSM527872", "GSM527873", "GSM527874", "GSM527875", "GSM527876", "GSM527877", "GSM527878", "GSM527879", "GSM527880", "GSM527881", "GSM527882", "GSM527883", "GSM527884", "GSM527885", "GSM527886", "GSM527887", "GSM527888", "GSM527889", "GSM527890", "GSM527891", "GSM527892", "GSM527893", "GSM527894", "GSM527895", "GSM527896", "GSM527897", "GSM527898", "GSM527899", "GSM527900", "GSM527901", "GSM527902", "GSM527903", "GSM527904", "GSM527905", "GSM527906", "GSM527907", "GSM527908", "GSM527909", "GSM527910", "GSM527911", "GSM527912", "GSM527913", "GSM527914", "GSM527915", "GSM527916", "GSM527917", "GSM527918", "GSM527919", "GSM527920", "GSM527921", "GSM527922", "GSM527923", "GSM527924", "GSM527925", "GSM527926", "GSM527927", "GSM527928", "GSM527929", "GSM527930", "GSM527931", "GSM527932", "GSM527933", "GSM527934", "GSM527935", "GSM527936", "GSM527937", "GSM527938", "GSM527939", "GSM527940", "GSM527941", "GSM527942", "GSM527943", "GSM527944", "GSM527945", "GSM527946", "GSM527947", "GSM527948", "GSM527949", "GSM527950", "GSM527951", "GSM527952", "GSM527953", "GSM527954", "GSM527955", "GSM527956", "GSM527957", "GSM527958", "GSM527959", "GSM527960", "GSM527961", "GSM527962", "GSM527963", "GSM527965", "GSM527966", "GSM527968", "GSM527970", "GSM527971", "GSM527972", "GSM527973", "GSM527974", "GSM527975", "GSM527977", "GSM527979", "GSM527980", "GSM527982", "GSM527984", "GSM527985", "GSM527986", "GSM527987", "GSM527988", "GSM527989", "GSM527990", "GSM527991", "GSM527992", "GSM527993", "GSM527994", "GSM527995", "GSM527996", "GSM527997", "GSM527998", "GSM527999", "GSM528000", "GSM528001", "GSM528002", "GSM528003", "GSM528004", "GSM528005", "GSM528006", "GSM528007", "GSM528008", "GSM528009", "GSM528010", "GSM528011", "GSM528012", "GSM528013", "GSM528014", "GSM528015", "GSM528016", "GSM528017", "GSM528018", "GSM528019", "GSM528020", "GSM528021", "GSM528022", "GSM528023", "GSM528024", "GSM528025", "GSM528026", "GSM528027", "GSM528028", "GSM528029", "GSM528030", "GSM528031", "GSM528032", "GSM528033", "GSM528034", "GSM528035", "GSM528036", "GSM528037", "GSM528038", "GSM528039", "GSM528040", "GSM528041", "GSM528042", "GSM528043", "GSM528044", "GSM528045", "GSM528046", "GSM528047", "GSM528048", "GSM528049"], "sample_count": 743, "group_sizes": null, "group_sizes_basis": null, "platform": "10264;8227;5188;4091", "taxon": "Homo sapiens", "title": "Integrative genomic profiling of human prostate cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE21032 not downloaded", "asset:data:geo:GSE21032 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-2", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "Protein-protein interaction"}}, {"id": "method-4", "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"}}, {"id": "method-5", "family": null, "specific": null, "label": "Cox proportional hazard regression analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "In our study, the key genes associated with overall survival (OS) were screened out from the top 25 candidate hub genes by Cox proportional hazard regression analysis based on the TCGA dataset."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE21032"], "resolved_accessions": ["GSE21032"], "statements": ["The original contributions presented in the study are included in the article/Supplementary Material, further inquiries can be directed to the corresponding authors."], "basis": "The paper names GSE21032 in c-BioPortal and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:35360870", "data:geo:GSE21032"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21032"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:40:17Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10573, "completion_tokens": 1127, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35360870", "type": "paper", "label": "pmid:35360870"}, {"id": "source:pmid:35360870", "type": "manuscript", "label": "PMID 35360870 full text"}, {"id": "data:geo:GSE21032", "type": "dataset", "label": "GEO GSE21032"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35360870", "type": "paper", "label": "pmid:35360870"}, {"id": "source:pmid:35360870", "type": "manuscript", "label": "PMID 35360870 full text"}, {"id": "data:geo:GSE21032", "type": "dataset", "label": "GEO GSE21032"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35360870", "type": "extraction", "used": ["source:pmid:35360870"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21032", "type": "accession_resolution", "used": ["data:geo:GSE21032"], "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:35360870", "parent_hash": "sha256:2d0802a748b42f53f5d17cc8f636df20dc970b5b5566cccf36e981860edc0af7", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE21032 licence not read", "asset:data:geo:GSE21032 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "analysis_only", "id": "assay:1"}]}