← All .science files
pmid:35002288
ADAMTS8 Expression is a Potential Prognostic Biomarker for Postoperative Metastasis in Lymph Node-Negative Early-Stage Invasive Breast Carcinoma Patients.
Yao Li · Xin Yang · Jie Sun · Yangyang Zhao · Qi Zhou · Bin Hua
Pharmacogenomics and personalized medicine · 2021 doi:10.2147/PGPM.S339919
Paper
complete
Experiment
complete
Data
partial
Analysis
partial
Execution
absent
Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
paper object · 10 fields
authors array · 6 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
assets array · 3 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 327 items
[2] object · 15 fields
structure object · 15 fields
sample_accessions array · 741 items
gaps array · 4 items
analysis object · 4 fields
methods array · 7 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 4 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[2] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 1 field
data_shapes array · 1 item
[3] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[4] object · 10 fields
dsl_operations array · 3 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[5] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[6] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
targets array · 0 items
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 2 items
resolved_accessions array · 2 items
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 2 items
steps array · 1 item
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 9 items
assays array · 4 items
[0] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[1] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 3 items
[2] object · 11 fields
required_operations array · 0 items
source_hashes object · 1 field
evidence array · 1 item
[3] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35002288", "kind": "science-record", "revision": 5, "content_hash": "sha256:f283cc4ab18269f48f0a7bd9e984c36be13b5fb5ce1c978e70b786e473c07223", "created_at": "2026-11-01T17:36:43Z", "updated_at": "2026-11-01T22:48:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "ADAMTS8 Expression is a Potential Prognostic Biomarker for Postoperative Metastasis in Lymph Node-Negative Early-Stage Invasive Breast Carcinoma Patients.", "doi": "10.2147/PGPM.S339919", "pmid": "35002288", "authors": ["Yao Li", "Xin Yang", "Jie Sun", "Yangyang Zhao", "Qi Zhou", "Bin Hua"], "journal": "Pharmacogenomics and personalized medicine", "year": 2021, "abstract": "PURPOSE: Invasive breast carcinoma (BC) is the most common malignant breast tumor. Most lymph node-negative (LN-) early-stage BC patients usually have a good prognosis, but 7% of patients still develop metastasis after surgery. It is not yet clear how to screen candidates with poorer prognosis in LN- early-stage patients, so that they can receive intensive therapy. Hence, we expect to identify a prognostic biomarker to assess postoperative metastasis in LN- early-stage BC patients.\nPATIENTS AND METHODS: Screening and verifying of candidate genes by gene expression profiling of LN- early-stage BC samples (n = 640) from 3 independent public datasets. Univariable and multivariable Cox regression analyses showed the relation between the candidate genes and postoperative metastasis. Distant metastasis-free survival (DMFS) analysis was performed to examine the prognostic significance. Quantitative real-time polymerase chain reaction (qRT-PCR) assays were performed to examine ADAMTS8 expression and prognostic association in our clinical samples (n = 25).\nRESULTS: In the discovery cohort (TCGA and GSE20685 datasets), we found that ADAMTS8 tend to be low expression in LN- early-stage BC, and low ADAMTS8 expression was associated with postoperative metastasis and shortened DMFS. Moreover, the above finding was confirmed in the validation cohort (GSE6538 dataset). Lower ADAMTS8 expression was related to poorer prognostic clinical stage and PAM50 subtypes and shorter DMFS. Gene enrichment analysis indicated that ADAMTS8 may be correlated with BC metastasis. qRT-PCR assays of our clinical tumor sample showed that patients with low ADAMTS8 expression seem to be prone to developing metastasis and have a shorter DMFS time.\nCONCLUSION: Our research shows that low ADAMTS8 expression is associated with postoperative metastasis and shortened DMFS in LN- early-stage BC patients, which suggests that ADAMTS8 may be a potential prognostic marker for postoperative metastasis in LN- early-stage BC patients.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier survival curves were used to compare the high and low expression groups according to the hazard ratio (HR) and log-rank p value.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35002288", "locator": "sections[7] \"Distant Metastasis-Free Survival Analysis\" paragraph 2", "quote": "Kaplan–Meier survival curves were used to compare the high and low expression groups according to the hazard ratio (HR) and log-rank p value."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Transcriptome and clinical data from BC patients were downloaded from TCGA (https://portal.gdc.cancer.gov/), and the microarray gene expression profiles and clinical data were retrieved from the GEO (GSE20685, GSE6532) (https://www.ncbi.nlm.nih.gov/gds) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35002288", "locator": "sections[3] \"Data Extraction\" paragraph 2", "quote": "Transcriptome and clinical data from BC patients were downloaded from TCGA (https://portal.gdc.cancer.gov/), and the microarray gene expression profiles and clinical data were retrieved from the GEO (GSE20685, GSE6532) (https://www.ncbi.nlm.nih.gov/gds) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We found that low ADAMTS8 expression was a high risk factor for postoperative metastasis in both discovery datasets (TCGA: HR = 5.637 [1.915–16.595], p = 0.002; GSE20685: HR = 14.550 [1.853–114.230], p = 0.011).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35002288", "locator": "sections[13] \"Identification of Candidate Gene in the Discovery Cohort\" paragraph 5", "quote": "We found that low ADAMTS8 expression was a high risk factor for postoperative metastasis in both discovery datasets (TCGA: HR = 5.637 [1.915–16.595], p = 0.002; GSE20685: HR = 14.550 [1.853–114.230], p = 0.011)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We found that low ADAMTS8 expression was a high risk factor for postoperative metastasis in both discovery datasets (TCGA: HR = 5.637 [1.915–16.595], p = 0.002; GSE20685: HR = 14.550 [1.853–114.230], p = 0.011).", "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:35002288"], "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:GSE20685"], "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:GSE20685"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35002288", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/PGPM.S339919", "sha256": "sha256:187d51cf39ea70a9a42667f480353faedf113db1a4f18715d4fd8f397f9c4fab", "bytes": 35786, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/PGPM.S339919", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8722701", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20685", "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=GSE20685", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20685", "version": null, "note": "Transcriptome and clinical data from BC patients were downloaded from TCGA (https://portal.gdc.cancer.gov/), and the microarray gene expression profiles and clinical data were retrieved from the GEO (GSE20685, GSE6532) (https://www.ncbi.nlm.nih.gov/gds) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Transcriptome and clinical data from BC patients were downloaded from TCGA (https://portal.gdc.cancer.gov/), and the microarray gene expression profiles and clinical data were retrieved from the GEO (GSE20685, GSE6532) (https://www.ncbi.nlm.nih.gov/gds) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM519117", "GSM519118", "GSM519119", "GSM519120", "GSM519121", "GSM519122", "GSM519123", "GSM519124", "GSM519125", "GSM519126", "GSM519127", "GSM519128", "GSM519129", "GSM519130", "GSM519131", "GSM519132", "GSM519133", "GSM519134", "GSM519135", "GSM519136", "GSM519137", "GSM519138", "GSM519139", "GSM519140", "GSM519141", "GSM519142", "GSM519143", "GSM519144", "GSM519145", "GSM519146", "GSM519147", "GSM519148", "GSM519149", "GSM519150", "GSM519151", "GSM519152", "GSM519153", "GSM519154", "GSM519155", "GSM519156", "GSM519157", "GSM519158", "GSM519159", "GSM519160", "GSM519161", "GSM519162", "GSM519163", "GSM519164", "GSM519165", "GSM519166", "GSM519167", "GSM519168", "GSM519169", "GSM519170", "GSM519171", "GSM519172", "GSM519173", "GSM519174", "GSM519175", "GSM519176", "GSM519177", "GSM519178", "GSM519179", "GSM519180", "GSM519181", "GSM519182", "GSM519183", "GSM519184", "GSM519185", "GSM519186", "GSM519187", "GSM519188", "GSM519189", "GSM519190", "GSM519191", "GSM519192", "GSM519193", "GSM519194", "GSM519195", "GSM519196", "GSM519197", "GSM519198", "GSM519199", "GSM519200", "GSM519201", "GSM519202", "GSM519203", "GSM519204", "GSM519205", "GSM519206", "GSM519207", "GSM519208", "GSM519209", "GSM519210", "GSM519211", "GSM519212", "GSM519213", "GSM519214", "GSM519215", "GSM519216", "GSM519217", "GSM519218", "GSM519219", "GSM519220", "GSM519221", "GSM519222", "GSM519223", "GSM519224", "GSM519225", "GSM519226", "GSM519227", "GSM519228", "GSM519229", "GSM519230", "GSM519231", "GSM519232", "GSM519233", "GSM519234", "GSM519235", "GSM519236", "GSM519237", "GSM519238", "GSM519239", "GSM519240", "GSM519241", "GSM519242", "GSM519243", "GSM519244", "GSM519245", "GSM519246", "GSM519247", "GSM519248", "GSM519249", "GSM519250", "GSM519251", "GSM519252", "GSM519253", "GSM519254", "GSM519255", "GSM519256", "GSM519257", "GSM519258", "GSM519259", "GSM519260", "GSM519261", "GSM519262", "GSM519263", "GSM519264", "GSM519265", "GSM519266", "GSM519267", "GSM519268", "GSM519269", "GSM519270", "GSM519271", "GSM519272", "GSM519273", "GSM519274", "GSM519275", "GSM519276", "GSM519277", "GSM519278", "GSM519279", "GSM519280", "GSM519281", "GSM519282", "GSM519283", "GSM519284", "GSM519285", "GSM519286", "GSM519287", "GSM519288", "GSM519289", "GSM519290", "GSM519291", "GSM519292", "GSM519293", "GSM519294", "GSM519295", "GSM519296", "GSM519297", "GSM519298", "GSM519299", "GSM519300", "GSM519301", "GSM519302", "GSM519303", "GSM519304", "GSM519305", "GSM519306", "GSM519307", "GSM519308", "GSM519309", "GSM519310", "GSM519311", "GSM519312", "GSM519313", "GSM519314", "GSM519315", "GSM519316", "GSM519317", "GSM519318", "GSM519319", "GSM519320", "GSM519321", "GSM519322", "GSM519323", "GSM519324", "GSM519325", "GSM519326", "GSM519327", "GSM519328", "GSM519329", "GSM519330", "GSM519331", "GSM519332", "GSM519333", "GSM519334", "GSM519335", "GSM519336", "GSM519337", "GSM519338", "GSM519339", "GSM519340", "GSM519341", "GSM519342", "GSM519343", "GSM519344", "GSM519345", "GSM519346", "GSM519347", "GSM519348", "GSM519349", "GSM519350", "GSM519351", "GSM519352", "GSM519353", "GSM519354", "GSM519355", "GSM519356", "GSM519357", "GSM519358", "GSM519359", "GSM519360", "GSM519361", "GSM519362", "GSM519363", "GSM519364", "GSM519365", "GSM519366", "GSM519367", "GSM519368", "GSM519369", "GSM519370", "GSM519371", "GSM519372", "GSM519373", "GSM519374", "GSM519375", "GSM519376", "GSM519377", "GSM519378", "GSM519379", "GSM519380", "GSM519381", "GSM519382", "GSM519383", "GSM519384", "GSM519385", "GSM519386", "GSM519387", "GSM519388", "GSM519389", "GSM519390", "GSM519391", "GSM519392", "GSM519393", "GSM519394", "GSM519395", "GSM519396", "GSM519397", "GSM519398", "GSM519399", "GSM519400", "GSM519401", "GSM519402", "GSM519403", "GSM519404", "GSM519405", "GSM519406", "GSM519407", "GSM519408", "GSM519409", "GSM519410", "GSM519411", "GSM519412", "GSM519413", "GSM519414", "GSM519415", "GSM519416", "GSM519417", "GSM519418", "GSM519419", "GSM519420", "GSM519421", "GSM519422", "GSM519423", "GSM519424", "GSM519425", "GSM519426", "GSM519427", "GSM519428", "GSM519429", "GSM519430", "GSM519431", "GSM519432", "GSM519433", "GSM519434", "GSM519435", "GSM519436", "GSM519437", "GSM519438", "GSM519439", "GSM519440", "GSM519441", "GSM519442", "GSM519443"], "sample_count": 327, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Microarray-based molecular subtyping of 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:GSE6532", "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=GSE6532", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE6532", "version": null, "note": "Transcriptome and clinical data from BC patients were downloaded from TCGA (https://portal.gdc.cancer.gov/), and the microarray gene expression profiles and clinical data were retrieved from the GEO (GSE20685, GSE6532) (https://www.ncbi.nlm.nih.gov/gds) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Transcriptome and clinical data from BC patients were downloaded from TCGA (https://portal.gdc.cancer.gov/), and the microarray gene expression profiles and clinical data were retrieved from the GEO (GSE20685, GSE6532) (https://www.ncbi.nlm.nih.gov/gds) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM150794", "GSM150795", "GSM150796", "GSM150797", "GSM150798", "GSM150799", "GSM150800", "GSM150801", "GSM150802", "GSM150803", "GSM150804", "GSM150805", "GSM150806", "GSM150807", "GSM150808", "GSM150809", "GSM150810", "GSM150811", "GSM150812", "GSM150813", "GSM150814", "GSM150815", "GSM150816", "GSM150817", "GSM150818", "GSM150819", "GSM150820", "GSM150821", "GSM150822", "GSM150823", "GSM150824", "GSM150825", "GSM150826", "GSM150827", "GSM150828", "GSM150829", "GSM150830", "GSM150831", "GSM150832", "GSM150833", "GSM150834", "GSM150835", "GSM150836", "GSM150837", "GSM150838", "GSM150839", "GSM150840", "GSM150841", "GSM150842", "GSM150843", "GSM150844", "GSM150845", "GSM150846", "GSM150847", "GSM150848", "GSM150849", "GSM150850", "GSM150851", "GSM150852", "GSM150853", "GSM150854", "GSM150855", "GSM150856", "GSM150857", "GSM150858", "GSM150859", "GSM150860", "GSM150861", "GSM150862", "GSM150863", "GSM150864", "GSM150865", "GSM150866", "GSM150867", "GSM150868", "GSM150869", "GSM150870", "GSM150871", "GSM150872", "GSM150873", "GSM150874", "GSM150875", "GSM150876", "GSM150877", "GSM150878", "GSM150879", "GSM150880", "GSM150881", "GSM150882", "GSM150883", "GSM150884", "GSM150885", "GSM150886", "GSM150887", "GSM150888", "GSM150889", "GSM150890", "GSM150891", "GSM150892", "GSM150893", "GSM150894", "GSM150895", "GSM150896", "GSM150897", "GSM150898", "GSM150899", "GSM150900", "GSM150901", "GSM150902", "GSM150903", "GSM150904", "GSM150905", "GSM150906", "GSM150907", "GSM150908", "GSM150909", "GSM150910", "GSM150911", "GSM150912", "GSM150913", "GSM150914", "GSM150915", "GSM150916", "GSM150917", "GSM150918", "GSM150919", "GSM150920", "GSM150921", "GSM150922", "GSM150923", "GSM150924", "GSM150925", "GSM150926", "GSM150927", "GSM150928", "GSM150929", "GSM150930", "GSM150931", "GSM150932", "GSM150933", "GSM150934", "GSM150935", "GSM150936", "GSM150937", "GSM150938", "GSM150939", "GSM150940", "GSM150941", "GSM150942", "GSM150943", "GSM150944", "GSM150945", "GSM150946", "GSM150947", "GSM150948", "GSM150949", "GSM150950", "GSM150951", "GSM150952", "GSM150953", "GSM150954", "GSM150955", "GSM150956", "GSM150957", "GSM150958", "GSM150959", "GSM150960", "GSM150961", "GSM150962", "GSM150963", "GSM150964", "GSM150965", "GSM150966", "GSM150967", "GSM150968", "GSM150969", "GSM150970", "GSM150971", "GSM150972", "GSM150973", "GSM150974", "GSM150975", "GSM150976", "GSM150977", "GSM150978", "GSM150979", "GSM150980", "GSM150981", "GSM150982", "GSM150983", "GSM150984", "GSM150985", "GSM150986", "GSM150987", "GSM150988", "GSM150989", "GSM150990", "GSM150991", "GSM150992", "GSM150993", "GSM150994", "GSM150995", "GSM150996", "GSM150997", "GSM150998", "GSM150999", "GSM151000", "GSM151001", "GSM151002", "GSM151003", "GSM151004", "GSM151005", "GSM151006", "GSM151007", "GSM151008", "GSM151009", "GSM151010", "GSM151011", "GSM151012", "GSM151013", "GSM151014", "GSM151015", "GSM151016", "GSM151017", "GSM151018", "GSM151019", "GSM151020", "GSM151021", "GSM151022", "GSM151023", "GSM151024", "GSM151025", "GSM151026", "GSM151027", "GSM151028", "GSM151029", "GSM151030", "GSM151031", "GSM151032", "GSM151033", "GSM151034", "GSM151035", "GSM151036", "GSM151037", "GSM151038", "GSM151039", "GSM151040", "GSM151041", "GSM151042", "GSM151043", "GSM151044", "GSM151045", "GSM151046", "GSM151047", "GSM151048", "GSM151049", "GSM151050", "GSM151051", "GSM151052", "GSM151053", "GSM151054", "GSM151055", "GSM151056", "GSM151057", "GSM151058", "GSM151059", "GSM151060", "GSM151061", "GSM151062", "GSM151063", "GSM151064", "GSM151065", "GSM151066", "GSM151067", "GSM151068", "GSM151069", "GSM151070", "GSM151071", "GSM151072", "GSM151073", "GSM151074", "GSM151075", "GSM151076", "GSM151077", "GSM151078", "GSM151079", "GSM151080", "GSM151081", "GSM151082", "GSM151083", "GSM151084", "GSM151085", "GSM151086", "GSM151087", "GSM151088", "GSM151089", "GSM151090", "GSM151091", "GSM151092", "GSM151093", "GSM151094", "GSM151095", "GSM151096", "GSM151097", "GSM151098", "GSM151099", "GSM151100", "GSM151101", "GSM151102", "GSM151103", "GSM151104", "GSM151105", "GSM151106", "GSM151107", "GSM151108", "GSM151109", "GSM151110", "GSM151111", "GSM151112", "GSM151113", "GSM151114", "GSM151115", "GSM151116", "GSM151117", "GSM151118", "GSM151119", "GSM151120", "GSM151121", "GSM151122", "GSM151123", "GSM151124", "GSM151125", "GSM151126", "GSM151127", "GSM151128", "GSM151129", "GSM151130", "GSM151131", "GSM151132", "GSM151133", "GSM151134", "GSM151135", "GSM151136", "GSM151137", "GSM151138", "GSM151139", "GSM151140", "GSM151141", "GSM151142", "GSM151143", "GSM151144", "GSM151145", "GSM151146", "GSM151147", "GSM151148", "GSM151149", "GSM151150", "GSM151151", "GSM151152", "GSM151153", "GSM151154", "GSM151155", "GSM151156", "GSM151157", "GSM151158", "GSM151159", "GSM151160", "GSM151161", "GSM151162", "GSM151163", "GSM151164", "GSM151165", "GSM151166", "GSM151167", "GSM151168", "GSM151169", "GSM151170", "GSM151171", "GSM151172", "GSM151173", "GSM151174", "GSM151175", "GSM151176", "GSM151177", "GSM151178", "GSM151179", "GSM151180", "GSM151181", "GSM151182", "GSM151183", "GSM151184", "GSM151185", "GSM151186", "GSM151187", "GSM151188", "GSM151189", "GSM151190", "GSM151191", "GSM151192", "GSM151193", "GSM151194", "GSM151195", "GSM151196", "GSM151197", "GSM151198", "GSM151199", "GSM151200", "GSM151201", "GSM151202", "GSM151203", "GSM151204", "GSM151205", "GSM151206", "GSM151207", "GSM151208", "GSM151209", "GSM151210", "GSM151211", "GSM151212", "GSM151213", "GSM151214", "GSM151215", "GSM151216", "GSM151217", "GSM151218", "GSM151219", "GSM151220", "GSM151221", "GSM151222", "GSM151223", "GSM151224", "GSM151225", "GSM151226", "GSM151227", "GSM151228", "GSM151229", "GSM151230", "GSM151231", "GSM151232", "GSM151233", "GSM151234", "GSM151235", "GSM151236", "GSM151237", "GSM151238", "GSM151239", "GSM151240", "GSM151241", "GSM151242", "GSM151243", "GSM151244", "GSM151245", "GSM151246", "GSM151247", "GSM151248", "GSM151249", "GSM151250", "GSM151251", "GSM151252", "GSM151253", "GSM151254", "GSM151255", "GSM151256", "GSM151257", "GSM151258", "GSM151259", "GSM151260", "GSM151261", "GSM151262", "GSM151263", "GSM151264", "GSM151265", "GSM151266", "GSM151267", "GSM151268", "GSM151269", "GSM151270", "GSM151271", "GSM151272", "GSM151273", "GSM151274", "GSM151275", "GSM151276", "GSM151277", "GSM151278", "GSM151279", "GSM151280", "GSM151281", "GSM151282", "GSM151283", "GSM151284", "GSM151285", "GSM151286", "GSM151287", "GSM151288", "GSM151289", "GSM151290", "GSM151291", "GSM151292", "GSM151293", "GSM151294", "GSM151295", "GSM151296", "GSM151297", "GSM151298", "GSM151299", "GSM151300", "GSM151301", "GSM151302", "GSM151303", "GSM151304", "GSM151305", "GSM151306", "GSM151307", "GSM151308", "GSM151309", "GSM151310", "GSM151311", "GSM151312", "GSM151313", "GSM151314", "GSM151315", "GSM151316", "GSM151317", "GSM151318", "GSM151319", "GSM151320", "GSM151321", "GSM151322", "GSM151323", "GSM151324", "GSM151325", "GSM151326", "GSM151327", "GSM151328", "GSM151329", "GSM151330", "GSM151331", "GSM151332", "GSM151333", "GSM151334", "GSM151335", "GSM151336", "GSM151337", "GSM151338", "GSM151339", "GSM151340", "GSM151341", "GSM151342", "GSM151343", "GSM151344", "GSM151345", "GSM65316", "GSM65317", "GSM65318", "GSM65319", "GSM65320", "GSM65321", "GSM65322", "GSM65323", "GSM65324", "GSM65325", "GSM65326", "GSM65327", "GSM65328", "GSM65329", "GSM65330", "GSM65331", "GSM65332", "GSM65333", "GSM65334", "GSM65335", "GSM65336", "GSM65337", "GSM65338", "GSM65339", "GSM65340", "GSM65341", "GSM65342", "GSM65343", "GSM65344", "GSM65345", "GSM65346", "GSM65347", "GSM65348", "GSM65349", "GSM65350", "GSM65351", "GSM65352", "GSM65353", "GSM65354", "GSM65355", "GSM65356", "GSM65357", "GSM65358", "GSM65359", "GSM65360", "GSM65361", "GSM65362", "GSM65363", "GSM65364", "GSM65365", "GSM65366", "GSM65367", "GSM65368", "GSM65369", "GSM65370", "GSM65371", "GSM65372", "GSM65373", "GSM65374", "GSM65375", "GSM65376", "GSM65377", "GSM65378", "GSM65379", "GSM65752", "GSM65753", "GSM65754", "GSM65755", "GSM65756", "GSM65757", "GSM65758", "GSM65760", "GSM65761", "GSM65762", "GSM65763", "GSM65764", "GSM65765", "GSM65766", "GSM65767", "GSM65768", "GSM65769", "GSM65770", "GSM65771", "GSM65772", "GSM65773", "GSM65774", "GSM65775", "GSM65776", "GSM65779", "GSM65780", "GSM65781", "GSM65782", "GSM65783", "GSM65784", "GSM65785", "GSM65786", "GSM65787", "GSM65788", "GSM65789", "GSM65790", "GSM65791", "GSM65792", "GSM65793", "GSM65794", "GSM65795", "GSM65796", "GSM65797", "GSM65798", "GSM65799", "GSM65800", "GSM65801", "GSM65802", "GSM65803", "GSM65804", "GSM65805", "GSM65806", "GSM65807", "GSM65808", "GSM65810", "GSM65811", "GSM65812", "GSM65813", "GSM65814", "GSM65815", "GSM65816", "GSM65817", "GSM65818", "GSM65819", "GSM65820", "GSM65821", "GSM65822", "GSM65823", "GSM65824", "GSM65825", "GSM65826", "GSM65827", "GSM65828", "GSM65829", "GSM65830", "GSM65831", "GSM65832", "GSM65833", "GSM65834", "GSM65835", "GSM65836", "GSM65837", "GSM65838", "GSM65839", "GSM65840", "GSM65841", "GSM65842", "GSM65843", "GSM65844", "GSM65845", "GSM65846", "GSM65847", "GSM65848", "GSM65849", "GSM65850", "GSM65851", "GSM65852", "GSM65853", "GSM65854", "GSM65855", "GSM65856", "GSM65857", "GSM65858", "GSM65859", "GSM65860", "GSM65861", "GSM65862", "GSM65863", "GSM65864", "GSM65865", "GSM65866", "GSM65867", "GSM65868", "GSM65869", "GSM65870", "GSM65871", "GSM65872", "GSM65873", "GSM65874", "GSM65875", "GSM65876", "GSM65877", "GSM65878", "GSM65879", "GSM65880"], "sample_count": 741, "group_sizes": null, "group_sizes_basis": null, "platform": "96;97;570", "taxon": "Homo sapiens", "title": "Definition of clinically distinct molecular subtypes in estrogen receptor positive breast carcinomas using genomic grade", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE20685 not downloaded", "asset:data:geo:GSE20685 licence not read", "asset:data:geo:GSE6532 not downloaded", "asset:data:geo:GSE6532 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "Kaplan–Meier survival curves were used to compare the high and low expression groups according to the hazard ratio (HR) and log-rank p value."}}, {"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": "ANOVA"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"p_value": "cording to the log-rank p value"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-4", "family": "differential_expression", "specific": "edger", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "edgeR"}}, {"id": "method-5", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-6", "family": "regression_modelling", "specific": "ols", "label": "Regression modelling", "dsl_operations": ["ols_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "Linear regression"}}, {"id": "method-7", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE20685", "GSE6532"], "resolved_accessions": ["GSE20685", "GSE6532"], "statements": ["Transcriptome and clinical data from BC patients were downloaded from TCGA (https://portal.gdc.cancer.gov/), and the microarray gene expression profiles and clinical data were retrieved from the GEO (GSE20685, GSE6532) (https://www.ncbi.nlm.nih.gov/gds) database."], "basis": "The paper names GSE20685, GSE6532 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["cox_ph"], "assets": ["source:pmid:35002288", "data:geo:GSE20685"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20685"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:15:57Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 11396, "completion_tokens": 2411, "cached_tokens": 256}}, "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:35002288", "type": "paper", "label": "pmid:35002288"}, {"id": "source:pmid:35002288", "type": "manuscript", "label": "PMID 35002288 full text"}, {"id": "data:geo:GSE20685", "type": "dataset", "label": "GEO GSE20685"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35002288", "type": "paper", "label": "pmid:35002288"}, {"id": "source:pmid:35002288", "type": "manuscript", "label": "PMID 35002288 full text"}, {"id": "data:geo:GSE20685", "type": "dataset", "label": "GEO GSE20685"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35002288", "type": "extraction", "used": ["source:pmid:35002288"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20685", "type": "accession_resolution", "used": ["data:geo:GSE20685"], "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:35002288", "parent_hash": "sha256:d203ee87096fba0eb00322c109d0e6d34f51ec6b2ceb33c0732c13ee4ce2a7a1", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE20685 licence not read", "asset:data:geo:GSE20685 not downloaded", "asset:data:geo:GSE6532 licence not read", "asset:data:geo:GSE6532 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": 0.93, "evidence": ["nd Methods Data Processing The raw counts of RNA-sequencing data from the TCGA dataset were corrected an"], "order_basis": "paper_text_order:2183", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e used to process raw data of the Affymetrix microarray in the GSE20685 and GSE6532 datasets, includ", "cedures were used to process raw data of the Affymetrix microarray in the GSE20685 and GSE6532 datas", "summarization. Probes were annotated by the Affymetrix annotation files. The PAM50 gene expression"], "order_basis": "paper_text_order:2346", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["SYBR Premix Ex Taq (TaKaRa). The primers for qPCR were as follows: GAPDH: forward 5ʹ-GGAGCGAGA"], "order_basis": "paper_text_order:4668", "id": "assay:3"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Kaplan–Meier survival curves were used to compare the high and low expression groups according to the hazard ratio (HR) and log-rank p value."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}