Intra-Tumoral Angiogenesis Is Associated with Inflammation, Immune Reaction and Metastatic Recurrence in Breast Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32933189", "kind": "science-record", "revision": 8, "content_hash": "sha256:22889293970eaa517c445a9b52e268abe3970ca94953a8358926b493fe364e3e", "created_at": "2026-11-01T15:41:10Z", "updated_at": "2026-11-01T22:02:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Intra-Tumoral Angiogenesis Is Associated with Inflammation, Immune Reaction and Metastatic Recurrence in Breast Cancer.", "doi": "10.3390/ijms21186708", "pmid": "32933189", "authors": ["Masanori Oshi", "Stephanie Newman", "Yoshihisa Tokumaru", "Li Yan", "Ryusei Matsuyama", "Itaru Endo", "Masayuki Nagahashi", "Kazuaki Takabe"], "journal": "International journal of molecular sciences", "year": 2020, "abstract": "Angiogenesis is one of the hallmarks of cancer. We hypothesized that intra-tumoral angiogenesis correlates with inflammation and metastasis in breast cancer patients. To test this hypothesis, we generated an angiogenesis pathway score using gene set variation analysis and analyzed the tumor transcriptome of 3999 breast cancer patients from The Cancer Genome Atlas Breast Cancer (TCGA-BRCA), Molecular Taxonomy of Breast Cancer International Consortium (METABRIC), GSE20194, GSE25066, GSE32646, and GSE2034 cohorts. We found that the score correlated with expression of various angiogenesis-, vascular stability-, and sphingosine-1-phosphate (S1P)-related genes. Surprisingly, the angiogenesis score was not associated with breast cancer subtype, Nottingham pathological grade, clinical stage, response to neoadjuvant chemotherapy, or patient survival. However, a high score was associated with a low fraction of both favorable and unfavorable immune cell infiltrations except for dendritic cell and M2 macrophage, and with Leukocyte Fraction, Tumor Infiltrating Lymphocyte Regional Fraction and Lymphocyte Infiltration Signature scores. High-score tumors had significant enrichment for unfavorable inflammation-related gene sets (interleukin (IL)6, and tumor necrosis factor (TNF)α- and TGFβ-signaling), as well as metastasis-related gene sets (epithelial mesenchymal transition, and Hedgehog-, Notch-, and WNT-signaling). High score was significantly associated with metastatic recurrence particularly to brain and bone. In conclusion, using the angiogenesis pathway score, we found that intra-tumoral angiogenesis is associated with immune reaction, inflammation and metastasis-related pathways, and metastatic recurrence in breast cancer.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier curves with log-rank tests were used for survival analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32933189", "locator": "sections[13] \"4.3. Statistical Analysis\" paragraph 2", "quote": "Kaplan–Meier curves with log-rank tests were used for survival analyses."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32933189", "locator": "sections[11] \"4.1. Genetic Profiling and Clinical Information of Breast Cancer Cohorts\" paragraph 2", "quote": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61]."}], "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:32933189"], "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:GSE20194"], "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:GSE20194"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32933189", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/ijms21186708", "sha256": "sha256:a0ecd86c6834d1d96d008cce30308b41a161075404f7a4bb5e5068438f36bff9", "bytes": 53089, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/ijms21186708", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7555442", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20194", "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=GSE20194", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20194", "version": null, "note": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM505327", "GSM505328", "GSM505329", "GSM505330", "GSM505331", "GSM505333", "GSM505334", "GSM505335", "GSM505336", "GSM505337", "GSM505338", "GSM505339", "GSM505340", "GSM505341", "GSM505342", "GSM505343", "GSM505344", "GSM505345", "GSM505346", "GSM505347", "GSM505348", "GSM505349", "GSM505350", "GSM505351", "GSM505352", "GSM505353", "GSM505354", "GSM505355", "GSM505356", "GSM505357", "GSM505358", "GSM505359", "GSM505360", "GSM505361", "GSM505362", "GSM505363", "GSM505364", "GSM505365", "GSM505366", "GSM505367", "GSM505368", "GSM505369", "GSM505370", "GSM505371", "GSM505372", "GSM505373", "GSM505374", "GSM505375", "GSM505376", "GSM505377", "GSM505378", "GSM505379", "GSM505380", "GSM505381", "GSM505382", "GSM505383", "GSM505384", "GSM505385", "GSM505386", "GSM505387", "GSM505388", "GSM505389", "GSM505390", "GSM505391", "GSM505392", "GSM505393", "GSM505394", "GSM505395", "GSM505396", "GSM505397", "GSM505398", "GSM505399", "GSM505400", "GSM505401", "GSM505402", "GSM505403", "GSM505404", "GSM505405", "GSM505406", "GSM505407", "GSM505408", "GSM505409", "GSM505410", "GSM505411", "GSM505412", "GSM505413", "GSM505414", "GSM505415", "GSM505416", "GSM505417", "GSM505418", "GSM505419", "GSM505420", "GSM505421", "GSM505422", "GSM505423", "GSM505424", "GSM505425", "GSM505426", "GSM505427", "GSM505428", "GSM505429", "GSM505430", "GSM505431", "GSM505432", "GSM505433", "GSM505434", "GSM505435", "GSM505436", "GSM505437", "GSM505438", "GSM505439", "GSM505440", "GSM505441", "GSM505442", "GSM505443", "GSM505444", "GSM505445", "GSM505446", "GSM505447", "GSM505448", "GSM505449", "GSM505450", "GSM505451", "GSM505452", "GSM505453", "GSM505454", "GSM505455", "GSM505456", "GSM505457", "GSM505458", "GSM505459", "GSM505460", "GSM505461", "GSM505462", "GSM505463", "GSM505464", "GSM505465", "GSM505466", "GSM505467", "GSM505468", "GSM505469", "GSM505470", "GSM505471", "GSM505472", "GSM505473", "GSM505474", "GSM505475", "GSM505476", "GSM505477", "GSM505478", "GSM505479", "GSM505480", "GSM505481", "GSM505482", "GSM505483", "GSM505484", "GSM505485", "GSM505486", "GSM505487", "GSM505488", "GSM505489", "GSM505490", "GSM505491", "GSM505492", "GSM505493", "GSM505494", "GSM505495", "GSM505496", "GSM505497", "GSM505498", "GSM505499", "GSM505500", "GSM505501", "GSM505502", "GSM505503", "GSM505504", "GSM505505", "GSM505506", "GSM505507", "GSM505508", "GSM505509", "GSM505510", "GSM505511", "GSM505512", "GSM505513", "GSM505514", "GSM505515", "GSM505516", "GSM505517", "GSM505518", "GSM505519", "GSM505520", "GSM505521", "GSM505522", "GSM505523", "GSM505524", "GSM505525", "GSM505526", "GSM505527", "GSM505528", "GSM505529", "GSM505530", "GSM505531", "GSM505532", "GSM505533", "GSM505534", "GSM505535", "GSM505536", "GSM505537", "GSM505538", "GSM505539", "GSM505540", "GSM505541", "GSM505542", "GSM505543", "GSM505544", "GSM505545", "GSM505546", "GSM505547", "GSM505548", "GSM505549", "GSM505550", "GSM505551", "GSM505552", "GSM505553", "GSM505554", "GSM505555", "GSM505556", "GSM505557", "GSM505558", "GSM505559", "GSM505560", "GSM505561", "GSM505562", "GSM505563", "GSM505564", "GSM505565", "GSM505566", "GSM505567", "GSM505568", "GSM505569", "GSM505570", "GSM505571", "GSM505572", "GSM505573", "GSM505574", "GSM505575", "GSM505576", "GSM505577", "GSM505578", "GSM505579", "GSM505580", "GSM505581", "GSM505582", "GSM505583", "GSM505584", "GSM505585", "GSM505586", "GSM505587", "GSM505588", "GSM505589", "GSM505590", "GSM505591", "GSM505592", "GSM505593", "GSM505594", "GSM505595", "GSM505596", "GSM505597", "GSM505598", "GSM505599", "GSM505600", "GSM505601", "GSM505602", "GSM505603", "GSM505604", "GSM505605"], "sample_count": 278, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "MAQC-II Project: human breast cancer (BR) data set", "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:GSE2034", "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=GSE2034", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2034", "version": null, "note": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM36777", "GSM36778", "GSM36779", "GSM36780", "GSM36781", "GSM36782", "GSM36783", "GSM36784", "GSM36785", "GSM36786", "GSM36787", "GSM36788", "GSM36789", "GSM36790", "GSM36791", "GSM36792", "GSM36793", "GSM36794", "GSM36795", "GSM36796", "GSM36797", "GSM36798", "GSM36799", "GSM36800", "GSM36801", "GSM36802", "GSM36803", "GSM36804", "GSM36805", "GSM36806", "GSM36807", "GSM36808", "GSM36809", "GSM36810", "GSM36811", "GSM36812", "GSM36813", "GSM36814", "GSM36815", "GSM36816", "GSM36817", "GSM36818", "GSM36819", "GSM36820", "GSM36821", "GSM36822", "GSM36823", "GSM36824", "GSM36825", "GSM36826", "GSM36827", "GSM36828", "GSM36829", "GSM36830", "GSM36831", "GSM36832", "GSM36833", "GSM36834", "GSM36835", "GSM36836", "GSM36837", "GSM36838", "GSM36839", "GSM36840", "GSM36841", "GSM36842", "GSM36843", "GSM36844", "GSM36845", "GSM36846", "GSM36847", "GSM36848", "GSM36849", "GSM36850", "GSM36851", "GSM36852", "GSM36853", "GSM36854", "GSM36855", "GSM36856", "GSM36857", "GSM36858", "GSM36859", "GSM36860", "GSM36861", "GSM36862", "GSM36863", "GSM36864", "GSM36865", "GSM36866", "GSM36867", "GSM36868", "GSM36869", "GSM36870", "GSM36871", "GSM36872", "GSM36873", "GSM36874", "GSM36875", "GSM36876", "GSM36877", "GSM36878", "GSM36879", "GSM36880", "GSM36881", "GSM36882", "GSM36883", "GSM36884", "GSM36885", "GSM36886", "GSM36887", "GSM36888", "GSM36889", "GSM36890", "GSM36891", "GSM36892", "GSM36893", "GSM36894", "GSM36895", "GSM36896", "GSM36897", "GSM36898", "GSM36899", "GSM36900", "GSM36901", "GSM36902", "GSM36903", "GSM36904", "GSM36905", "GSM36906", "GSM36907", "GSM36908", "GSM36909", "GSM36910", "GSM36911", "GSM36912", "GSM36913", "GSM36914", "GSM36915", "GSM36916", "GSM36917", "GSM36918", "GSM36919", "GSM36920", "GSM36921", "GSM36922", "GSM36923", "GSM36924", "GSM36925", "GSM36926", "GSM36927", "GSM36928", "GSM36929", "GSM36930", "GSM36931", "GSM36932", "GSM36933", "GSM36934", "GSM36935", "GSM36936", "GSM36937", "GSM36938", "GSM36939", "GSM36940", "GSM36941", "GSM36942", "GSM36943", "GSM36944", "GSM36945", "GSM36946", "GSM36947", "GSM36948", "GSM36949", "GSM36950", "GSM36951", "GSM36952", "GSM36953", "GSM36954", "GSM36955", "GSM36956", "GSM36957", "GSM36958", "GSM36959", "GSM36960", "GSM36961", "GSM36962", "GSM36963", "GSM36964", "GSM36965", "GSM36966", "GSM36967", "GSM36968", "GSM36969", "GSM36970", "GSM36971", "GSM36972", "GSM36973", "GSM36974", "GSM36975", "GSM36976", "GSM36977", "GSM36978", "GSM36979", "GSM36980", "GSM36981", "GSM36982", "GSM36983", "GSM36984", "GSM36985", "GSM36986", "GSM36987", "GSM36988", "GSM36989", "GSM36990", "GSM36991", "GSM36992", "GSM36993", "GSM36994", "GSM36995", "GSM36996", "GSM36997", "GSM36998", "GSM36999", "GSM37000", "GSM37001", "GSM37002", "GSM37003", "GSM37004", "GSM37005", "GSM37006", "GSM37007", "GSM37008", "GSM37009", "GSM37010", "GSM37011", "GSM37012", "GSM37013", "GSM37014", "GSM37015", "GSM37016", "GSM37017", "GSM37018", "GSM37019", "GSM37020", "GSM37021", "GSM37022", "GSM37023", "GSM37024", "GSM37025", "GSM37026", "GSM37027", "GSM37028", "GSM37029", "GSM37030", "GSM37031", "GSM37032", "GSM37033", "GSM37034", "GSM37035", "GSM37036", "GSM37037", "GSM37038", "GSM37039", "GSM37040", "GSM37041", "GSM37042", "GSM37043", "GSM37044", "GSM37045", "GSM37046", "GSM37047", "GSM37048", "GSM37049", "GSM37050", "GSM37051", "GSM37052", "GSM37053", "GSM37054", "GSM37055", "GSM37056", "GSM37057", "GSM37058", "GSM37059", "GSM37060", "GSM37061", "GSM37062"], "sample_count": 286, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Breast cancer relapse free survival", "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:GSE25066", "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=GSE25066", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25066", "version": null, "note": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM615096", "GSM615097", "GSM615098", "GSM615099", "GSM615100", "GSM615101", "GSM615102", "GSM615103", "GSM615104", "GSM615105", "GSM615106", "GSM615107", "GSM615108", "GSM615109", "GSM615110", "GSM615111", "GSM615112", "GSM615113", "GSM615114", "GSM615115", "GSM615116", "GSM615117", "GSM615118", "GSM615119", "GSM615120", "GSM615121", "GSM615122", "GSM615123", "GSM615124", "GSM615125", "GSM615126", "GSM615127", "GSM615128", "GSM615129", "GSM615130", "GSM615131", "GSM615132", "GSM615133", "GSM615134", "GSM615135", "GSM615136", "GSM615137", "GSM615138", "GSM615139", "GSM615140", "GSM615141", "GSM615142", "GSM615143", "GSM615144", "GSM615145", "GSM615146", "GSM615147", "GSM615148", "GSM615149", "GSM615150", "GSM615151", "GSM615152", "GSM615153", "GSM615154", "GSM615155", "GSM615156", "GSM615157", "GSM615158", "GSM615159", "GSM615160", "GSM615161", "GSM615162", "GSM615163", "GSM615164", "GSM615165", "GSM615166", "GSM615167", "GSM615168", "GSM615169", "GSM615170", "GSM615171", "GSM615172", "GSM615173", "GSM615174", "GSM615175", "GSM615176", "GSM615177", "GSM615178", "GSM615179", "GSM615180", "GSM615181", "GSM615182", "GSM615183", "GSM615184", "GSM615185", "GSM615186", "GSM615187", "GSM615188", "GSM615189", "GSM615190", "GSM615191", "GSM615192", "GSM615193", "GSM615194", "GSM615195", "GSM615196", "GSM615197", "GSM615198", "GSM615199", "GSM615200", "GSM615201", "GSM615202", "GSM615203", "GSM615204", "GSM615205", "GSM615206", "GSM615207", "GSM615208", "GSM615209", "GSM615210", "GSM615211", "GSM615212", "GSM615213", "GSM615214", "GSM615215", "GSM615216", "GSM615217", "GSM615218", "GSM615219", "GSM615220", "GSM615221", "GSM615222", "GSM615223", "GSM615224", "GSM615225", "GSM615226", "GSM615227", "GSM615228", "GSM615229", "GSM615230", "GSM615231", "GSM615232", "GSM615233", "GSM615234", "GSM615235", "GSM615236", "GSM615237", "GSM615238", "GSM615239", "GSM615240", "GSM615241", "GSM615242", "GSM615243", "GSM615244", "GSM615245", "GSM615246", "GSM615247", "GSM615248", "GSM615249", "GSM615250", "GSM615251", "GSM615252", "GSM615253", "GSM615254", "GSM615255", "GSM615256", "GSM615257", "GSM615258", "GSM615259", "GSM615260", "GSM615261", "GSM615262", "GSM615263", "GSM615264", "GSM615265", "GSM615266", "GSM615267", "GSM615268", "GSM615269", "GSM615270", "GSM615271", "GSM615272", "GSM615273", "GSM615274", "GSM615275", "GSM615276", "GSM615277", "GSM615278", "GSM615279", "GSM615280", "GSM615281", "GSM615282", "GSM615283", "GSM615284", "GSM615285", "GSM615286", "GSM615287", "GSM615288", "GSM615289", "GSM615290", "GSM615291", "GSM615292", "GSM615293", "GSM615294", "GSM615295", "GSM615296", "GSM615297", "GSM615298", "GSM615299", "GSM615300", "GSM615301", "GSM615302", "GSM615303", "GSM615304", "GSM615305", "GSM615306", "GSM615307", "GSM615308", "GSM615309", "GSM615310", "GSM615311", "GSM615312", "GSM615313", "GSM615314", "GSM615315", "GSM615316", "GSM615317", "GSM615318", "GSM615319", "GSM615320", "GSM615321", "GSM615322", "GSM615323", "GSM615324", "GSM615325", "GSM615326", "GSM615327", "GSM615328", "GSM615329", "GSM615330", "GSM615331", "GSM615332", "GSM615333", "GSM615334", "GSM615335", "GSM615336", "GSM615337", "GSM615338", "GSM615339", "GSM615340", "GSM615341", "GSM615342", "GSM615343", "GSM615344", "GSM615345", "GSM615346", "GSM615347", "GSM615348", "GSM615349", "GSM615350", "GSM615351", "GSM615352", "GSM615353", "GSM615354", "GSM615355", "GSM615356", "GSM615357", "GSM615358", "GSM615359", "GSM615360", "GSM615361", "GSM615362", "GSM615363", "GSM615364", "GSM615365", "GSM615366", "GSM615367", "GSM615368", "GSM615369", "GSM615370", "GSM615371", "GSM615372", "GSM615373", "GSM615374", "GSM615375", "GSM615376", "GSM615377", "GSM615378", "GSM615379", "GSM615380", "GSM615381", "GSM615382", "GSM615383", "GSM615384", "GSM615385", "GSM615386", "GSM615387", "GSM615388", "GSM615389", "GSM615390", "GSM615391", "GSM615392", "GSM615393", "GSM615394", "GSM615395", "GSM615396", "GSM615397", "GSM615398", "GSM615399", "GSM615400", "GSM615401", "GSM615402", "GSM615403", "GSM615404", "GSM615405", "GSM615631", "GSM615632", "GSM615633", "GSM615634", "GSM615635", "GSM615636", "GSM615637", "GSM615638", "GSM615639", "GSM615640", "GSM615641", "GSM615642", "GSM615643", "GSM615644", "GSM615645", "GSM615646", "GSM615647", "GSM615648", "GSM615649", "GSM615650", "GSM615651", "GSM615652", "GSM615653", "GSM615654", "GSM615655", "GSM615656", "GSM615657", "GSM615658", "GSM615659", "GSM615660", "GSM615661", "GSM615662", "GSM615663", "GSM615664", "GSM615665", "GSM615666", "GSM615667", "GSM615668", "GSM615669", "GSM615670", "GSM615671", "GSM615672", "GSM615673", "GSM615674", "GSM615675", "GSM615676", "GSM615677", "GSM615678", "GSM615679", "GSM615680", "GSM615681", "GSM615682", "GSM615683", "GSM615684", "GSM615685", "GSM615686", "GSM615687", "GSM615688", "GSM615689", "GSM615690", "GSM615691", "GSM615692", "GSM615693", "GSM615694", "GSM615695", "GSM615696", "GSM615697", "GSM615698", "GSM615699", "GSM615700", "GSM615701", "GSM615702", "GSM615703", "GSM615704", "GSM615705", "GSM615706", "GSM615707", "GSM615708", "GSM615709", "GSM615710", "GSM615711", "GSM615712", "GSM615713", "GSM615714", "GSM615715", "GSM615716", "GSM615717", "GSM615718", "GSM615719", "GSM615720", "GSM615721", "GSM615722", "GSM615723", "GSM615724", "GSM615725", "GSM615726", "GSM615727", "GSM615728", "GSM615729", "GSM615730", "GSM615731", "GSM615732", "GSM615733", "GSM615734", "GSM615735", "GSM615736", "GSM615737", "GSM615738", "GSM615739", "GSM615740", "GSM615741", "GSM615742", "GSM615743", "GSM615744", "GSM615745", "GSM615746", "GSM615747", "GSM615748", "GSM615749", "GSM615750", "GSM615751", "GSM615752", "GSM615753", "GSM615754", "GSM615755", "GSM615756", "GSM615757", "GSM615758", "GSM615759", "GSM615760", "GSM615761", "GSM615762", "GSM615763", "GSM615764", "GSM615765", "GSM615766", "GSM615767", "GSM615768", "GSM615769", "GSM615770", "GSM615771", "GSM615772", "GSM615773", "GSM615774", "GSM615775", "GSM615776", "GSM615777", "GSM615778", "GSM615779", "GSM615780", "GSM615781", "GSM615782", "GSM615783", "GSM615784", "GSM615785", "GSM615786", "GSM615787", "GSM615788", "GSM615789", "GSM615790", "GSM615791", "GSM615792", "GSM615793", "GSM615794", "GSM615795", "GSM615796", "GSM615797", "GSM615798", "GSM615799", "GSM615800", "GSM615801", "GSM615802", "GSM615803", "GSM615804", "GSM615805", "GSM615806", "GSM615807", "GSM615808", "GSM615809", "GSM615810", "GSM615811", "GSM615812", "GSM615813", "GSM615814", "GSM615815", "GSM615816", "GSM615817", "GSM615818", "GSM615819", "GSM615820", "GSM615821", "GSM615822", "GSM615823", "GSM615824", "GSM615825", "GSM615826", "GSM615827", "GSM615828"], "sample_count": 508, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Genomic predictor of response and survival following neoadjuvant taxane-anthracycline chemotherapy in breast cancer", "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:GSE32646", "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=GSE32646", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32646", "version": null, "note": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61].", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM809184", "GSM809185", "GSM809186", "GSM809187", "GSM809188", "GSM809189", "GSM809190", "GSM809191", "GSM809192", "GSM809193", "GSM809194", "GSM809195", "GSM809196", "GSM809197", "GSM809198", "GSM809199", "GSM809200", "GSM809201", "GSM809202", "GSM809203", "GSM809204", "GSM809205", "GSM809206", "GSM809207", "GSM809208", "GSM809209", "GSM809210", "GSM809211", "GSM809212", "GSM809213", "GSM809214", "GSM809215", "GSM809216", "GSM809217", "GSM809218", "GSM809219", "GSM809220", "GSM809221", "GSM809222", "GSM809223", "GSM809224", "GSM809225", "GSM809226", "GSM809227", "GSM809228", "GSM809229", "GSM809230", "GSM809231", "GSM809232", "GSM809233", "GSM809234", "GSM809235", "GSM809236", "GSM809237", "GSM809238", "GSM809239", "GSM809240", "GSM809241", "GSM809242", "GSM809243", "GSM809244", "GSM809245", "GSM809246", "GSM809247", "GSM809248", "GSM809249", "GSM809250", "GSM809251", "GSM809252", "GSM809253", "GSM809254", "GSM809255", "GSM809256", "GSM809257", "GSM809258", "GSM809259", "GSM809260", "GSM809261", "GSM809262", "GSM809263", "GSM809264", "GSM809265", "GSM809266", "GSM809267", "GSM809268", "GSM809269", "GSM809270", "GSM809271", "GSM809272", "GSM809273", "GSM809274", "GSM809275", "GSM809276", "GSM809277", "GSM809278", "GSM809279", "GSM809280", "GSM809281", "GSM809282", "GSM809283", "GSM809284", "GSM809285", "GSM809286", "GSM809287", "GSM809288", "GSM809289", "GSM809290", "GSM809291", "GSM809292", "GSM809293", "GSM809294", "GSM809295", "GSM809296", "GSM809297", "GSM809298"], "sample_count": 115, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "GSTP1 expression predicts poor pathological complete response to neoadjuvant chemotherapy in ER-negative breast cancer", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32933189:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:0f9d648cc2151f3e91aa66696aa1c545a8f4b07d9b3fba9ab6466a3b36a9ffb2", "bytes": 705, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#array1", "version": null, "note": null, "structure": {"pmcid": "PMC7555442", "section_index": 16, "section_title": "Abbreviations", "row_count": 14, "column_count": 2}, "table": {"label": null, "caption": null, "rows": [["AJCC", "American Joint Committee on Cancer"], ["DFS", "disease-free survival"], ["DSS", "disease-specific survival"], ["ER", "estrogen receptor"], ["FDR", "false discovery rate"], ["GSVA", "gene set variation analysis"], ["HER2", "human epidermal growth factor receptor 2"], ["METABRIC", "Molecular Taxonomy of Breast Cancer International Consortium"], ["NES", "normalized enrichment score"], ["OS", "overall survival"], ["pCR", "pathological complete response"], ["PFS", "progression-free survival"], ["TCGA", "The Cancer Genome Atlas"], ["TNBC", "triple negative breast cancer"]], "row_count": 14, "column_count": 2, "numeric_cells": 1, "header_rows": 0, "locator": "section[16]/table-wrap[1]#array1"}}], "gaps": ["asset:data:geo:GSE20194 not downloaded", "asset:data:geo:GSE20194 licence not read", "asset:data:geo:GSE2034 not downloaded", "asset:data:geo:GSE2034 licence not read", "asset:data:geo:GSE25066 not downloaded", "asset:data:geo:GSE25066 licence not read", "asset:data:geo:GSE32646 not downloaded", "asset:data:geo:GSE32646 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Kaplan–Meier curves with log-rank tests were used for survival analyses."}}, {"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"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE20194", "GSE25066", "GSE32646", "GSE2034"], "resolved_accessions": ["GSE20194", "GSE25066", "GSE32646", "GSE2034"], "statements": ["The Cancer Genome Atlas Breast Cancer cohort (TCGA-BRCA) RNA-sequencing data and clinical information of 1065 patients, who were female and had pathological diagnosis of breast cancer, were obtained from Pan-Cancer Clinical Data Resource [33] and through the cBio Cancer Genomic Portal [61]."], "basis": "The paper names GSE20194, GSE25066, GSE32646, GSE2034 in Gene Expression Omnibus (GEO) repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:32933189", "data:geo:GSE20194", "asset:table:pmid:32933189:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20194"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:22:35Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 43368, "completion_tokens": 2774, "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:32933189", "type": "paper", "label": "pmid:32933189"}, {"id": "source:pmid:32933189", "type": "manuscript", "label": "PMID 32933189 full text"}, {"id": "data:geo:GSE20194", "type": "dataset", "label": "GEO GSE20194"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32933189", "type": "paper", "label": "pmid:32933189"}, {"id": "source:pmid:32933189", "type": "manuscript", "label": "PMID 32933189 full text"}, {"id": "data:geo:GSE20194", "type": "dataset", "label": "GEO GSE20194"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32933189", "type": "extraction", "used": ["source:pmid:32933189"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20194", "type": "accession_resolution", "used": ["data:geo:GSE20194"], "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:32933189", "parent_hash": "sha256:973f2b7c68485355ce6206a671f733377a11745323d69fa09c95db6a097da5d1", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE20194 licence not read", "asset:data:geo:GSE20194 not downloaded", "asset:data:geo:GSE2034 licence not read", "asset:data:geo:GSE2034 not downloaded", "asset:data:geo:GSE25066 licence not read", "asset:data:geo:GSE25066 not downloaded", "asset:data:geo:GSE32646 licence not read", "asset:data:geo:GSE32646 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["et variation analysis and analyzed the tumor transcriptome of 3999 breast cancer patients from The Canc"], "order_basis": "paper_text_order:367", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan–Meier curves with log-rank tests were used for survival analyses."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}