{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33693962", "kind": "science-record", "revision": 3, "content_hash": "sha256:17fb398d2cd20c8ea4abf22b9b6f62ecd3c32258eb9f101a1a35ec5e0e3138f3", "created_at": "2026-11-01T17:34:53Z", "updated_at": "2026-11-01T21:24:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "New insights for precision treatment of glioblastoma from analysis of single-cell lncRNA expression.", "doi": "10.1007/s00432-021-03584-9", "pmid": "33693962", "authors": ["Qingkang Meng", "Yan Zhang", "Guoqi Li", "Yunong Li", "Hongbo Xie", "Xiujie Chen"], "journal": "Journal of cancer research and clinical oncology", "year": 2021, "abstract": "INTRODUCTION: Glioblastoma (GBM) is a complex disease with high intratumoral heterogeneity, understanding the molecular characteristics of intratumoral heterogeneity accurately is the basis for precision treatment. Although the existing typing strategy based on tumor molecular characteristics has a positive effect, there is still room for improvement, which is mainly because the traditional typing is completed based on the sequencing data of tissue samples, that is, the obtained data are the average level of patient tumor tissues, masking the intratumoral heterogeneity of a single patient and cannot reflect the real level of patient tumor cells. At present, cancer molecular typing is mostly performed based on transcriptome (RNA-seq) without considering lncRNA molecules that are also tissue-specific and developmental stage-specific. Therefore, in this study, we used lncRNAs as typing markers and combined single-cell expression profiles to retype glioblastoma, providing new ideas for GBM molecular typing, and further analyzed the shortcomings of traditional therapies at the singlecell level based on typing results and proposed new precise therapeutic insights.\nMETHODS: We downloaded GBM single-cell sequencing data from GSE84465 and performed a series of preprocessing. The intratumoral heterogeneity of patients at the single-cell level was revealed using t-SNE, and the room for improvement of the existing traditional histotyping method was revealed using heat map and density curve. Subsequently, to validate the feasibility of lncRNA typing, we compared the similarities and differences of expression patterns between lncRNAs and mRNAs in GBM cells. Then, we used the R package \"Seurat\" to perform unsupervised clustering of GBM cells for re-typing and performed a detailed analysis of the biological characteristics of each subtype, including differentially expressed lncRNAs and marker lncRNAs. For validation, we performed survival analysis on GBM tissue data from the TCGA database to reveal the impact of different subtypes on patient survival prognosis. Eventually, based on the results, we screened the therapeutic drugs of each subtype by targeting the downstream regulatory genes of lncRNAs and proposed a new precision therapeutic strategy.\nRESULTS: GBM has significant intratumoral heterogeneity at the single-cell level, with more than one traditional subtype highly expressed in each patient, which reflects the shortcomings of traditional histotyping. LncRNAs and mRNAs have similar expression patterns in GBM cells, and the expression coefficient of variation of lncRNAs is higher than that of mRNAs, meaning that lncRNAs will better reflect the intratumoral heterogeneity. GBM was reclassified into four subtypes by unsupervised clustering, with different subtypes having different biological characteristics. Survival analysis showed that patients with different subtype compositions had different prognostic outcomes, so different subtypes had different effects on patient prognosis. Based on this, 47 drugs were screened for treatment. There are both shared and unique drugs between different subtypes. A new precision treatment strategy was proposed: for patients with different subtypes, in addition to the combination of drugs targeting single subtype, drugs targeting multiple subtypes can also be selected.\nCONCLUSION: Intratumoral heterogeneity may lead to poor prognosis or recurrence after treatment, and more precise typing of GBM can be performed based on single-cell lncRNA expression profiles. The biological characteristics possessed by different subtypes will have different effects on patients, such as survival time. For different subtypes, there are both drugs targeting single subtype and drugs targeting multiple subtypes, and we prefer drugs targeting multiple subtypes because this strategy can maximize medication efficiency and reduce the types of medication to reduce risks and side effects.", "claims": [{"id": "claim-method", "statement": "Then, we used the R package “Seurat” to perform unsupervised clustering of GBM cells for re-typing and performed a detailed analysis of the biological characteristics of each subtype, including differentially expressed lncRNAs and marker lncRNAs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33693962", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Then, we used the R package “Seurat” to perform unsupervised clustering of GBM cells for re-typing and performed a detailed analysis of the biological characteristics of each subtype, including differentially expressed lncRNAs and marker lncRNAs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded GBM single-cell sequencing data from GSE84465 and performed a series of preprocessing.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33693962", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We downloaded GBM single-cell sequencing data from GSE84465 and performed a series of preprocessing."}], "state": "complete"}, {"id": "claim-target-result", "statement": "GBM was reclassified into four subtypes by unsupervised clustering, with different subtypes having different biological characteristics.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:33693962", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "GBM was reclassified into four subtypes by unsupervised clustering, with different subtypes having different biological characteristics."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "GBM was reclassified into four subtypes by unsupervised clustering, with different subtypes having different biological characteristics.", "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:33693962"], "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:GSE84465"], "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:GSE84465"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33693962", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s00432-021-03584-9", "sha256": "sha256:492990d3c3733f8cd84a720ea828f0771ee4894a9181d36bce20a245512b3294", "bytes": 4017, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s00432-021-03584-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11802005", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE84465", "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=GSE84465", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE84465", "version": null, "note": "We downloaded GBM single-cell sequencing data from GSE84465 and performed a series of preprocessing.", "structure": {"repository": 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"GSM2244279", "GSM2244280", "GSM2244281", "GSM2244282", "GSM2244283", "GSM2244284", "GSM2244285", "GSM2244286", "GSM2244287", "GSM2244288", "GSM2244289", "GSM2244290", "GSM2244291", "GSM2244292", "GSM2244293", "GSM2244294", "GSM2244295", "GSM2244296", "GSM2244297", "GSM2244298", "GSM2244299", "GSM2244300", "GSM2244301", "GSM2244302", "GSM2244303", "GSM2244304", "GSM2244305", "GSM2244306", "GSM2244307", "GSM2244308", "GSM2244309", "GSM2244310", "GSM2244311", "GSM2244312", "GSM2244313", "GSM2244314", "GSM2244315", "GSM2244316", "GSM2244317", "GSM2244318", "GSM2244319", "GSM2244320", "GSM2244321", "GSM2244322", "GSM2244323", "GSM2244324", "GSM2244325", "GSM2244326", "GSM2244327", "GSM2244328", "GSM2244329", "GSM2244330", "GSM2244331", "GSM2244332", "GSM2244333", "GSM2244334", "GSM2244335", "GSM2244336", "GSM2244337", "GSM2244338", "GSM2244339", "GSM2244340", "GSM2244341", "GSM2244342", "GSM2244343", "GSM2244344", "GSM2244345", "GSM2244346", "GSM2244347", "GSM2244348", "GSM2244349", "GSM2244350", "GSM2244351", "GSM2244352", "GSM2244353", "GSM2244354", "GSM2244355", "GSM2244356", "GSM2244357", "GSM2244358", "GSM2244359", "GSM2244360", "GSM2244361", "GSM2244362", "GSM2244363", "GSM2244364", "GSM2244365", "GSM2244366", "GSM2244367", "GSM2244368", "GSM2244369", "GSM2244370", "GSM2244371", "GSM2244372", "GSM2244373", "GSM2244374", "GSM2244375", "GSM2244376", "GSM2244377", "GSM2244378", "GSM2244379", "GSM2244380", "GSM2244381", "GSM2244382", "GSM2244383", "GSM2244384", "GSM2244385", "GSM2244386", "GSM2244387", "GSM2244388", "GSM2244389", "GSM2244390", "GSM2244391", "GSM2244392", "GSM2244393", "GSM2244394", "GSM2244395", "GSM2244396", "GSM2244397", "GSM2244398", "GSM2244399", "GSM2244400", "GSM2244401", "GSM2244402", "GSM2244403", "GSM2244404", "GSM2244405", "GSM2244406", "GSM2244407", "GSM2244408", "GSM2244409", "GSM2244410", "GSM2244411", "GSM2244412", "GSM2244413", "GSM2244414", "GSM2244415", "GSM2244416", "GSM2244417", "GSM2244418", "GSM2244419", "GSM2244420", "GSM2244421", "GSM2244422", "GSM2244423", "GSM2244424", "GSM2244425", "GSM2244426", "GSM2244427", "GSM2244428", "GSM2244429", "GSM2244430", "GSM2244431", "GSM2244432", "GSM2244433", "GSM2244434", "GSM2244435", "GSM2244436", "GSM2244437", "GSM2244438", "GSM2244439", "GSM2244440", "GSM2244441", "GSM2244442", "GSM2244443", "GSM2244444", "GSM2244445", "GSM2244446", "GSM2244447", "GSM2244448", "GSM2244449", "GSM2244450", "GSM2244451", "GSM2244452", "GSM2244453", "GSM2244454", "GSM2244455", "GSM2244456", "GSM2244457", "GSM2244458", "GSM2244459", "GSM2244460", "GSM2244461", "GSM2244462", "GSM2244463", "GSM2244464", "GSM2244465", "GSM2244466", "GSM2244467", "GSM2244468", "GSM2244469", "GSM2244470", "GSM2244471", "GSM2244472", "GSM2244473", "GSM2244474", "GSM2244475", "GSM2244476", "GSM2244477", "GSM2244478", "GSM2244479", "GSM2244480", "GSM2244481", "GSM2244482", "GSM2244483", "GSM2244484", "GSM2244485", "GSM2244486", "GSM2244487", "GSM2244488", "GSM2244489", "GSM2244490", "GSM2244491", "GSM2244492", "GSM2244493", "GSM2244494", "GSM2244495", "GSM2244496", "GSM2244497", "GSM2244498", "GSM2244499", "GSM2244500", "GSM2244501", "GSM2244502", "GSM2244503", "GSM2244504", "GSM2244505", "GSM2244506", "GSM2244507", "GSM2244508", "GSM2244509", "GSM2244510", "GSM2244511", "GSM2244512", "GSM2244513", "GSM2244514", "GSM2244515", "GSM2244516", "GSM2244517", "GSM2244518", "GSM2244519", "GSM2244520", "GSM2244521", "GSM2244522", "GSM2244523", "GSM2244524", "GSM2244525", "GSM2244526", "GSM2244527", "GSM2244528", "GSM2244529", "GSM2244530", "GSM2244531", "GSM2244532", "GSM2244533", "GSM2244534", "GSM2244535", "GSM2244536", "GSM2244537", "GSM2244538", "GSM2244539", "GSM2244540", "GSM2244541", "GSM2244542", "GSM2244543", "GSM2244544", "GSM2244545", "GSM2244546", "GSM2244547", "GSM2244548", "GSM2244549", "GSM2244550", "GSM2244551", "GSM2244552", "GSM2244553", "GSM2244554", "GSM2244555", "GSM2244556", "GSM2244557", "GSM2244558", "GSM2244559", "GSM2244560", "GSM2244561", "GSM2244562", "GSM2244563", "GSM2244564", "GSM2244565", "GSM2244566", "GSM2244567", "GSM2244568", "GSM2244569", "GSM2244570", "GSM2244571", "GSM2244572", "GSM2244573", "GSM2244574", "GSM2244575", "GSM2244576", "GSM2244577", "GSM2244578", "GSM2244579", "GSM2244580", "GSM2244581", "GSM2244582", "GSM2244583", "GSM2244584", "GSM2244585", "GSM2244586", "GSM2244587", "GSM2244588", "GSM2244589", "GSM2244590", "GSM2244591", "GSM2244592", "GSM2244593", "GSM2244594", "GSM2244595", "GSM2244596", "GSM2244597", "GSM2244598", "GSM2244599", "GSM2244600", "GSM2244601", "GSM2244602", "GSM2244603", "GSM2244604", "GSM2244605", "GSM2244606", "GSM2244607", "GSM2244608", "GSM2244609", "GSM2244610", "GSM2244611", "GSM2244612", "GSM2244613", "GSM2244614", "GSM2244615", "GSM2244616", "GSM2244617", "GSM2244618", "GSM2244619", "GSM2244620", "GSM2244621", "GSM2244622", "GSM2244623", "GSM2244624", "GSM2244625", "GSM2244626", "GSM2244627", "GSM2244628", "GSM2244629", "GSM2244630", "GSM2244631", "GSM2244632", "GSM2244633", "GSM2244634", "GSM2244635", "GSM2244636", "GSM2244637", "GSM2244638", "GSM2244639", "GSM2244640", "GSM2244641", "GSM2244642", "GSM2244643", "GSM2244644", "GSM2244645", "GSM2244646", "GSM2244647", "GSM2244648", "GSM2244649", "GSM2244650", "GSM2244651", "GSM2244652", "GSM2244653", "GSM2244654", "GSM2244655", "GSM2244656", "GSM2244657", "GSM2244658", "GSM2244659", "GSM2244660", "GSM2244661", "GSM2244662", "GSM2244663", "GSM2244664", "GSM2244665", "GSM2244666", "GSM2244667", "GSM2244668", "GSM2244669", "GSM2244670", "GSM2244671", "GSM2244672", "GSM2244673", "GSM2244674", "GSM2244675", "GSM2244676", "GSM2244677", "GSM2244678", "GSM2244679", "GSM2244680", "GSM2244681", "GSM2244682", "GSM2244683", "GSM2244684", "GSM2244685", "GSM2244686", "GSM2244687", "GSM2244688", "GSM2244689", "GSM2244690", "GSM2244691", "GSM2244692", "GSM2244693", "GSM2244694", "GSM2244695", "GSM2244696", "GSM2244697", "GSM2244698", "GSM2244699", "GSM2244700", "GSM2244701", "GSM2244702", "GSM2244703", "GSM2244704", "GSM2244705", "GSM2244706", "GSM2244707", "GSM2244708", "GSM2244709", "GSM2244710", "GSM2244711", "GSM2244712", "GSM2244713", "GSM2244714", "GSM2244715", "GSM2244716", "GSM2244717", "GSM2244718", "GSM2244719", "GSM2244720", "GSM2244721", "GSM2244722", "GSM2244723", "GSM2244724", "GSM2244725", "GSM2244726", "GSM2244727", "GSM2244728", "GSM2244729", "GSM2244730", "GSM2244731", "GSM2244732", "GSM2244733", "GSM2244734", "GSM2244735", "GSM2244736", "GSM2244737", "GSM2244738", "GSM2244739", "GSM2244740", "GSM2244741", "GSM2244742", "GSM2244743", "GSM2244744", "GSM2244745", "GSM2244746", "GSM2244747", "GSM2244748", "GSM2244749", "GSM2244750", "GSM2244751", "GSM2244752", "GSM2244753", "GSM2244754", "GSM2244755", "GSM2244756", "GSM2244757", "GSM2244758", "GSM2244759", "GSM2244760", "GSM2244761", "GSM2244762", "GSM2244763", "GSM2244764", "GSM2244765", "GSM2244766", "GSM2244767", "GSM2244768", "GSM2244769", "GSM2244770", "GSM2244771", "GSM2244772", "GSM2244773", "GSM2244774", "GSM2244775", "GSM2244776", "GSM2244777", "GSM2244778", "GSM2244779", "GSM2244780", "GSM2244781", "GSM2244782", "GSM2244783", "GSM2244784", "GSM2244785", "GSM2244786", "GSM2244787", "GSM2244788", "GSM2244789", "GSM2244790", "GSM2244791", "GSM2244792", "GSM2244793", "GSM2244794", "GSM2244795", "GSM2244796", "GSM2244797", "GSM2244798", "GSM2244799", "GSM2244800", "GSM2244801", "GSM2244802", "GSM2244803", "GSM2244804", "GSM2244805", "GSM2244806", "GSM2244807", "GSM2244808", "GSM2244809", "GSM2244810", "GSM2244811", "GSM2244812", "GSM2244813", "GSM2244814", "GSM2244815", "GSM2244816", "GSM2244817", "GSM2244818", "GSM2244819", "GSM2244820", "GSM2244821", "GSM2244822", "GSM2244823", "GSM2244824", "GSM2244825", "GSM2244826", "GSM2244827", "GSM2244828", "GSM2244829", "GSM2244830", "GSM2244831", "GSM2244832", "GSM2244833", "GSM2244834", "GSM2244835", "GSM2244836", "GSM2244837", "GSM2244838", "GSM2244839", "GSM2244840", "GSM2244841", "GSM2244842", "GSM2244843", "GSM2244844", "GSM2244845", "GSM2244846", "GSM2244847", "GSM2244848", "GSM2244849", "GSM2244850", "GSM2244851", "GSM2244852", "GSM2244853", "GSM2244854", "GSM2244855", "GSM2244856", "GSM2244857", "GSM2244858", "GSM2244859", "GSM2244860", "GSM2244861", "GSM2244862", "GSM2244863", "GSM2244864", "GSM2244865", "GSM2244866", "GSM2244867", "GSM2244868", "GSM2244869", "GSM2244870", "GSM2244871", "GSM2244872", "GSM2244873", "GSM2244874", "GSM2244875", "GSM2244876", "GSM2244877", "GSM2244878", "GSM2244879", "GSM2244880", "GSM2244881", "GSM2244882", "GSM2244883", "GSM2244884", "GSM2244885", "GSM2244886", "GSM2244887", "GSM2244888", "GSM2244889", "GSM2244890", "GSM2244891", "GSM2244892", "GSM2244893", "GSM2244894", "GSM2244895", "GSM2244896", "GSM2244897", "GSM2244898", "GSM2244899", "GSM2244900", "GSM2244901", "GSM2244902", "GSM2244903", "GSM2244904", "GSM2244905", "GSM2244906", "GSM2244907", "GSM2244908", "GSM2244909", "GSM2244910", "GSM2244911", "GSM2244912", "GSM2244913", "GSM2244914", "GSM2244915", "GSM2244916", "GSM2244917", "GSM2244918", "GSM2244919", "GSM2244920", "GSM2244921", "GSM2244922", "GSM2244923", "GSM2244924", "GSM2244925", "GSM2244926", "GSM2244927", "GSM2244928", "GSM2244929", "GSM2244930", "GSM2244931", "GSM2244932", "GSM2244933", "GSM2244934", "GSM2244935", "GSM2244936", "GSM2244937", "GSM2244938", "GSM2244939", "GSM2244940", "GSM2244941", "GSM2244942", "GSM2244943", "GSM2244944", "GSM2244945", "GSM2244946", "GSM2244947", "GSM2244948", "GSM2244949", "GSM2244950", "GSM2244951", "GSM2244952", "GSM2244953", "GSM2244954", "GSM2244955", "GSM2244956", "GSM2244957", "GSM2244958", "GSM2244959", "GSM2244960", "GSM2244961", "GSM2244962", "GSM2244963", "GSM2244964", "GSM2244965", "GSM2244966", "GSM2244967", "GSM2244968", "GSM2244969", "GSM2244970", "GSM2244971", "GSM2244972", "GSM2244973", "GSM2244974", "GSM2244975", "GSM2244976", "GSM2244977", "GSM2244978", "GSM2244979", "GSM2244980", "GSM2244981", "GSM2244982", "GSM2244983", "GSM2244984", "GSM2244985", "GSM2244986", "GSM2244987", "GSM2244988", "GSM2244989", "GSM2244990", "GSM2244991", "GSM2244992", "GSM2244993", "GSM2244994", "GSM2244995", "GSM2244996", "GSM2244997", "GSM2244998", "GSM2244999", "GSM2245000", "GSM2245001", "GSM2245002", "GSM2245003", "GSM2245004", "GSM2245005", "GSM2245006", "GSM2245007", "GSM2245008", "GSM2245009", "GSM2245010", "GSM2245011", "GSM2245012", "GSM2245013", "GSM2245014", "GSM2245015", "GSM2245016", "GSM2245017", "GSM2245018", "GSM2245019", "GSM2245020", "GSM2245021", "GSM2245022", "GSM2245023", "GSM2245024", "GSM2245025", "GSM2245026", "GSM2245027", "GSM2245028", "GSM2245029", "GSM2245030", "GSM2245031", "GSM2245032", "GSM2245033", "GSM2245034", "GSM2245035", "GSM2245036", "GSM2245037", "GSM2245038", "GSM2245039", "GSM2245040", "GSM2245041", "GSM2245042", "GSM2245043", "GSM2245044", "GSM2245045", "GSM2245046", "GSM2245047", "GSM2245048", "GSM2245049", "GSM2245050", "GSM2245051", "GSM2245052", "GSM2245053", "GSM2245054", "GSM2245055", "GSM2245056", "GSM2245057", "GSM2245058", "GSM2245059", "GSM2245060", "GSM2245061", "GSM2245062", "GSM2245063", "GSM2245064", "GSM2245065", "GSM2245066", "GSM2245067", "GSM2245068", "GSM2245069", "GSM2245070", "GSM2245071", "GSM2245072", "GSM2245073", "GSM2245074", "GSM2245075", "GSM2245076", "GSM2245077", "GSM2245078", "GSM2245079", "GSM2245080", "GSM2245081", "GSM2245082", "GSM2245083", "GSM2245084", "GSM2245085", "GSM2245086", "GSM2245087", "GSM2245088", "GSM2245089", "GSM2245090", "GSM2245091", "GSM2245092", "GSM2245093", "GSM2245094", "GSM2245095", "GSM2245096", "GSM2245097", "GSM2245098", "GSM2245099", "GSM2245100", "GSM2245101", "GSM2245102", "GSM2245103", "GSM2245104", "GSM2245105", "GSM2245106", "GSM2245107", "GSM2245108", "GSM2245109", "GSM2245110", "GSM2245111", "GSM2245112", "GSM2245113", "GSM2245114", "GSM2245115", "GSM2245116", "GSM2245117", "GSM2245118", "GSM2245119", "GSM2245120", "GSM2245121", "GSM2245122", "GSM2245123", "GSM2245124", "GSM2245125", "GSM2245126", "GSM2245127", "GSM2245128", "GSM2245129", "GSM2245130", "GSM2245131", "GSM2245132", "GSM2245133", "GSM2245134", "GSM2245135", "GSM2245136", "GSM2245137", "GSM2245138", "GSM2245139", "GSM2245140", "GSM2245141", "GSM2245142", "GSM2245143", "GSM2245144", "GSM2245145", "GSM2245146", "GSM2245147", "GSM2245148", "GSM2245149", "GSM2245150", "GSM2245151", "GSM2245152", "GSM2245153", "GSM2245154", "GSM2245155", "GSM2245156", "GSM2245157", "GSM2245158", "GSM2245159", "GSM2245160", "GSM2245161", "GSM2245162", "GSM2245163", "GSM2245164", "GSM2245165", "GSM2245166", "GSM2245167", "GSM2245168", "GSM2245169", "GSM2245170", "GSM2245171", "GSM2245172", "GSM2245173", "GSM2245174", "GSM2245175", "GSM2245176", "GSM2245177", "GSM2245178", "GSM2245179", "GSM2245180", "GSM2245181", "GSM2245182", "GSM2245183", "GSM2245184", "GSM2245185", "GSM2245186", "GSM2245187", "GSM2245188", "GSM2245189", "GSM2245190", "GSM2245191", "GSM2245192", "GSM2245193", "GSM2245194", "GSM2245195", "GSM2245196", "GSM2245197", "GSM2245198", "GSM2245199", "GSM2245200", "GSM2245201", "GSM2245202", "GSM2245203", "GSM2245204", "GSM2245205", "GSM2245206", "GSM2245207", "GSM2245208", "GSM2245209", "GSM2245210", "GSM2245211", "GSM2245212", "GSM2245213", "GSM2245214", "GSM2245215", "GSM2245216", "GSM2245217", "GSM2245218", "GSM2245219", "GSM2245220", "GSM2245221", "GSM2245222", "GSM2245223", "GSM2245224", "GSM2245225", "GSM2245226", "GSM2245227", "GSM2245228", "GSM2245229", "GSM2245230", "GSM2245231", "GSM2245232", "GSM2245233", "GSM2245234", "GSM2245235", "GSM2245236", "GSM2245237", "GSM2245238", "GSM2245239", "GSM2245240", "GSM2245241", "GSM2245242", "GSM2245243", "GSM2245244", "GSM2245245", "GSM2245246", "GSM2245247", "GSM2245248", "GSM2245249", "GSM2245250", "GSM2245251", "GSM2245252", "GSM2245253", "GSM2245254", "GSM2245255", "GSM2245256", "GSM2245257", "GSM2245258", "GSM2245259", "GSM2245260", "GSM2245261", "GSM2245262", "GSM2245263", "GSM2245264", "GSM2245265", "GSM2245266", "GSM2245267", "GSM2245268", "GSM2245269", "GSM2245270", "GSM2245271", "GSM2245272", "GSM2245273", "GSM2245274", "GSM2245275", "GSM2245276", "GSM2245277", "GSM2245278", "GSM2245279", "GSM2245280", "GSM2245281", "GSM2245282", "GSM2245283", "GSM2245284", "GSM2245285", "GSM2245286", "GSM2245287", "GSM2245288", "GSM2245289", "GSM2245290", "GSM2245291", "GSM2245292", "GSM2245293", "GSM2245294", "GSM2245295", "GSM2245296", "GSM2245297", "GSM2245298", "GSM2245299", "GSM2245300", "GSM2245301", "GSM2245302", "GSM2245303", "GSM2245304", "GSM2245305", "GSM2245306", "GSM2245307", "GSM2245308", "GSM2245309", "GSM2245310", "GSM2245311", "GSM2245312", "GSM2245313", "GSM2245314", "GSM2245315", "GSM2245316", "GSM2245317", "GSM2245318", "GSM2245319", "GSM2245320", "GSM2245321", "GSM2245322", "GSM2245323", "GSM2245324", "GSM2245325", "GSM2245326", "GSM2245327", "GSM2245328", "GSM2245329", "GSM2245330", "GSM2245331", "GSM2245332", "GSM2245333", "GSM2245334", "GSM2245335", "GSM2245336", "GSM2245337", "GSM2245338", "GSM2245339", "GSM2245340", "GSM2245341", "GSM2245342", "GSM2245343", "GSM2245344", "GSM2245345", "GSM2245346", "GSM2245347", "GSM2245348", "GSM2245349", "GSM2245350", "GSM2245351", "GSM2245352", "GSM2245353", "GSM2245354", "GSM2245355", "GSM2245356", "GSM2245357", "GSM2245358", "GSM2245359", "GSM2245360", "GSM2245361", "GSM2245362", "GSM2245363", "GSM2245364", "GSM2245365", "GSM2245366", "GSM2245367", "GSM2245368", "GSM2245369", "GSM2245370", "GSM2245371", "GSM2245372", "GSM2245373", "GSM2245374", "GSM2245375", "GSM2245376", "GSM2245377", "GSM2245378", "GSM2245379", "GSM2245380", "GSM2245381", "GSM2245382", "GSM2245383", "GSM2245384", "GSM2245385", "GSM2245386", "GSM2245387", "GSM2245388", "GSM2245389", "GSM2245390", "GSM2245391", "GSM2245392", "GSM2245393", "GSM2245394", "GSM2245395", "GSM2245396", "GSM2245397", "GSM2245398", "GSM2245399", "GSM2245400", "GSM2245401", "GSM2245402", "GSM2245403", "GSM2245404", "GSM2245405", "GSM2245406", "GSM2245407", "GSM2245408", "GSM2245409", "GSM2245410", "GSM2245411", "GSM2245412", "GSM2245413", "GSM2245414", "GSM2245415", "GSM2245416", "GSM2245417", "GSM2245418", "GSM2245419", "GSM2245420", "GSM2245421", "GSM2245422", "GSM2245423", "GSM2245424", "GSM2245425", "GSM2245426", "GSM2245427", "GSM2245428", "GSM2245429", "GSM2245430", "GSM2245431", "GSM2245432", "GSM2245433", "GSM2245434", "GSM2245435", "GSM2245436", "GSM2245437", "GSM2245438", "GSM2245439", "GSM2245440", "GSM2245441", "GSM2245442", "GSM2245443", "GSM2245444", "GSM2245445", "GSM2245446", "GSM2245447", "GSM2245448", "GSM2245449", "GSM2245450", "GSM2245451", "GSM2245452", "GSM2245453", "GSM2245454", "GSM2245455", "GSM2245456", "GSM2245457", "GSM2245458", "GSM2245459", "GSM2245460", "GSM2245461", "GSM2245462", "GSM2245463", "GSM2245464", "GSM2245465", "GSM2245466", "GSM2245467", "GSM2245468", "GSM2245469", "GSM2245470", "GSM2245471", "GSM2245472", "GSM2245473", "GSM2245474", "GSM2245475", "GSM2245476", "GSM2245477", "GSM2245478", "GSM2245479", "GSM2245480", "GSM2245481", "GSM2245482", "GSM2245483", "GSM2245484", "GSM2245485", "GSM2245486", "GSM2245487", "GSM2245488", "GSM2245489", "GSM2245490", "GSM2245491", "GSM2245492", "GSM2245493", "GSM2245494", "GSM2245495", "GSM2245496", "GSM2245497", "GSM2245498", "GSM2245499", "GSM2245500", "GSM2245501", "GSM2245502", "GSM2245503", "GSM2245504", "GSM2245505", "GSM2245506", "GSM2245507", "GSM2245508", "GSM2245509", "GSM2245510", "GSM2245511", "GSM2245512", "GSM2245513", "GSM2245514", "GSM2245515", "GSM2245516", "GSM2245517", "GSM2245518", "GSM2245519", "GSM2245520", "GSM2245521", "GSM2245522", "GSM2245523", "GSM2245524", "GSM2245525", "GSM2245526", "GSM2245527", "GSM2245528", "GSM2245529", "GSM2245530", "GSM2245531", "GSM2245532", "GSM2245533", "GSM2245534", "GSM2245535", "GSM2245536", "GSM2245537", "GSM2245538", "GSM2245539", "GSM2245540", "GSM2245541", "GSM2245542", "GSM2245543", "GSM2245544", "GSM2245545", "GSM2245546", "GSM2245547", "GSM2245548", "GSM2245549", "GSM2245550", "GSM2245551", "GSM2245552", "GSM2245553", "GSM2245554", "GSM2245555", "GSM2245556", "GSM2245557", "GSM2245558", "GSM2245559", "GSM2245560", "GSM2245561", "GSM2245562", "GSM2245563", "GSM2245564", "GSM2245565", "GSM2245566", "GSM2245567", "GSM2245568", "GSM2245569", "GSM2245570", "GSM2245571", "GSM2245572", "GSM2245573", "GSM2245574", "GSM2245575", "GSM2245576", "GSM2245577", "GSM2245578", "GSM2245579", "GSM2245580", "GSM2245581", "GSM2245582", "GSM2245583", "GSM2245584", "GSM2245585", "GSM2245586", "GSM2245587", "GSM2245588", "GSM2245589", "GSM2245590", "GSM2245591", "GSM2245592", "GSM2245593", "GSM2245594", "GSM2245595", "GSM2245596", "GSM2245597", "GSM2245598", "GSM2245599", "GSM2245600", "GSM2245601", "GSM2245602", "GSM2245603", "GSM2245604", "GSM2245605", "GSM2245606", "GSM2245607", "GSM2245608", "GSM2245609", "GSM2245610", "GSM2245611", "GSM2245612", "GSM2245613", "GSM2245614", "GSM2245615", "GSM2245616", "GSM2245617", "GSM2245618", "GSM2245619", "GSM2245620", "GSM2245621", "GSM2245622", "GSM2245623", "GSM2245624", "GSM2245625", "GSM2245626", "GSM2245627", "GSM2245628", "GSM2245629", "GSM2245630", "GSM2245631", "GSM2245632", "GSM2245633", "GSM2245634", "GSM2245635", "GSM2245636", "GSM2245637", "GSM2245638", "GSM2245639", "GSM2245640", "GSM2245641", "GSM2245642", "GSM2245643", "GSM2245644", "GSM2245645", "GSM2245646", "GSM2245647", "GSM2245648", "GSM2245649", "GSM2245650", "GSM2245651", "GSM2245652", "GSM2245653", "GSM2245654", "GSM2245655", "GSM2245656", "GSM2245657", "GSM2245658", "GSM2245659", "GSM2245660", "GSM2245661", "GSM2245662", "GSM2245663", "GSM2245664", "GSM2245665", "GSM2245666", "GSM2245667", "GSM2245668", "GSM2245669", "GSM2245670", "GSM2245671", "GSM2245672", "GSM2245673", "GSM2245674", "GSM2245675", "GSM2245676", "GSM2245677", "GSM2245678", "GSM2245679", "GSM2245680", "GSM2245681", "GSM2245682", "GSM2245683", "GSM2245684", "GSM2245685", "GSM2245686", "GSM2245687", "GSM2245688", "GSM2245689", "GSM2245690", "GSM2245691", "GSM2245692", "GSM2245693", "GSM2245694", "GSM2245695", "GSM2245696", "GSM2245697", "GSM2245698", "GSM2245699", "GSM2245700", "GSM2245701", "GSM2245702", "GSM2245703", "GSM2245704", "GSM2245705", "GSM2245706", "GSM2245707", "GSM2245708", "GSM2245709", "GSM2245710", "GSM2245711", "GSM2245712", "GSM2245713", "GSM2245714", "GSM2245715", "GSM2245716", "GSM2245717", "GSM2245718", "GSM2245719", "GSM2245720", "GSM2245721", "GSM2245722", "GSM2245723", "GSM2245724", "GSM2245725", "GSM2245726", "GSM2245727", "GSM2245728", "GSM2245729", "GSM2245730", "GSM2245731", "GSM2245732", "GSM2245733", "GSM2245734", "GSM2245735", "GSM2245736", "GSM2245737", "GSM2245738", "GSM2245739", "GSM2245740", "GSM2245741", "GSM2245742", "GSM2245743", "GSM2245744", "GSM2245745", "GSM2245746", "GSM2245747", "GSM2245748", "GSM2245749", "GSM2245750", "GSM2245751", "GSM2245752", "GSM2245753", "GSM2245754", "GSM2245755", "GSM2245756", "GSM2245757", "GSM2245758", "GSM2245759", "GSM2245760", "GSM2245761", "GSM2245762", "GSM2245763", "GSM2245764", "GSM2245765", "GSM2245766", "GSM2245767", "GSM2245768", "GSM2245769", "GSM2245770", "GSM2245771", "GSM2245772", "GSM2245773", "GSM2245774", "GSM2245775", "GSM2245776", "GSM2245777", "GSM2245778", "GSM2245779", "GSM2245780", "GSM2245781", "GSM2245782", "GSM2245783", "GSM2245784", "GSM2245785", "GSM2245786", "GSM2245787", "GSM2245788", "GSM2245789", "GSM2245790", "GSM2245791", "GSM2245792", "GSM2245793", "GSM2245794", "GSM2245795", "GSM2245796", "GSM2245797", "GSM2245798", "GSM2245799", "GSM2245800", "GSM2245801", "GSM2245802", "GSM2245803", "GSM2245804", "GSM2245805", "GSM2245806", "GSM2245807", "GSM2245808", "GSM2245809", "GSM2245810", "GSM2245811", "GSM2245812", "GSM2245813", "GSM2245814", "GSM2245815", "GSM2245816", "GSM2245817", "GSM2245818", "GSM2245819", "GSM2245820", "GSM2245821", "GSM2245822", "GSM2245823", "GSM2245824", "GSM2245825", "GSM2245826", "GSM2245827", "GSM2245828", "GSM2245829", "GSM2245830", "GSM2245831", "GSM2245832", "GSM2245833", "GSM2245834", "GSM2245835", "GSM2245836", "GSM2245837", "GSM2245838", "GSM2245839", "GSM2245840", "GSM2245841", "GSM2245842", "GSM2245843", "GSM2245844", "GSM2245845", "GSM2245846", "GSM2245847", "GSM2245848", "GSM2245849", "GSM2245850", "GSM2245851", "GSM2245852", "GSM2245853", "GSM2245854", "GSM2245855", "GSM2245856", "GSM2245857", "GSM2245858", "GSM2245859", "GSM2245860", "GSM2245861", "GSM2245862", "GSM2245863", "GSM2245864", "GSM2245865", "GSM2245866", "GSM2245867", "GSM2245868", "GSM2245869", "GSM2245870", "GSM2245871", "GSM2245872", "GSM2245873", "GSM2245874", "GSM2245875", "GSM2245876", "GSM2245877", "GSM2245878", "GSM2245879", "GSM2245880", "GSM2245881", "GSM2245882", "GSM2245883", "GSM2245884", "GSM2245885", "GSM2245886", "GSM2245887", "GSM2245888", "GSM2245889", "GSM2245890", "GSM2245891", "GSM2245892", "GSM2245893", "GSM2245894", "GSM2245895", "GSM2245896", "GSM2245897", "GSM2245898", "GSM2245899", "GSM2245900", "GSM2245901", "GSM2245902", "GSM2245903", "GSM2245904", "GSM2245905", "GSM2245906", "GSM2245907", "GSM2245908", "GSM2245909", "GSM2245910", "GSM2245911", "GSM2245912", "GSM2245913", "GSM2245914", "GSM2245915", "GSM2245916", "GSM2245917", "GSM2245918", "GSM2245919", "GSM2245920", "GSM2245921", "GSM2245922", "GSM2245923", "GSM2245924", "GSM2245925", "GSM2245926", "GSM2245927", "GSM2245928", "GSM2245929", "GSM2245930", "GSM2245931", "GSM2245932", "GSM2245933", "GSM2245934", "GSM2245935", "GSM2245936", "GSM2245937", "GSM2245938", "GSM2245939", "GSM2245940", "GSM2245941", "GSM2245942", "GSM2245943", "GSM2245945", "GSM2245948", "GSM2245950", "GSM2245952", "GSM2245955", "GSM2245957", "GSM2245959", "GSM2245961", "GSM2245965", "GSM2245966", "GSM2245968", "GSM2245971", "GSM2245972", "GSM2245974", "GSM2245976", "GSM2245977", "GSM2245980", "GSM2245981", "GSM2245982", "GSM2245983", "GSM2245984", "GSM2245985", "GSM2245986", "GSM2245987", "GSM2245988", "GSM2245989", "GSM2245990", "GSM2245991", "GSM2245992", "GSM2245993", "GSM2245994", "GSM2245995", "GSM2245996", "GSM2245997", "GSM2245998", "GSM2245999", "GSM2246000", "GSM2246001", "GSM2246002", "GSM2246003", "GSM2246004", "GSM2246005", "GSM2246006", "GSM2246007", "GSM2246008", "GSM2246009", "GSM2246010", "GSM2246011", "GSM2246012", "GSM2246013", "GSM2246014", "GSM2246015", "GSM2246016", "GSM2246017", "GSM2246018", "GSM2246019", "GSM2246020", "GSM2246021", "GSM2246022", "GSM2246023", "GSM2246024", "GSM2246025", "GSM2246026", "GSM2246027", "GSM2246028", "GSM2246029", "GSM2246030", "GSM2246031", "GSM2246032", "GSM2246033", "GSM2246034", "GSM2246035", "GSM2246036", "GSM2246037", "GSM2246038", "GSM2246039", "GSM2246040", "GSM2246041", "GSM2246042", "GSM2246043", "GSM2246044", "GSM2246045", "GSM2246046", "GSM2246047", "GSM2246048", "GSM2246049", "GSM2246050", "GSM2246051", "GSM2246052", "GSM2246053", "GSM2246054", "GSM2246055", "GSM2246056", "GSM2246057", "GSM2246058", "GSM2246059", "GSM2246060", "GSM2246061", "GSM2246062", "GSM2246063", "GSM2246064", "GSM2246065", "GSM2246066", "GSM2246067", "GSM2246068", "GSM2246069", "GSM2246070", "GSM2246071", "GSM2246072", "GSM2246073", "GSM2246074", "GSM2246075", "GSM2246076", "GSM2246077", "GSM2246078", "GSM2246079", "GSM2246080", "GSM2246081", "GSM2246082", "GSM2246083", "GSM2246084", "GSM2246085", "GSM2246086", "GSM2246087", "GSM2246088", "GSM2246089", "GSM2246090", "GSM2246091", "GSM2246092", "GSM2246093", "GSM2246094", "GSM2246095", "GSM2246096", "GSM2246097", "GSM2246098", "GSM2246099", "GSM2246100", "GSM2246101", "GSM2246102", "GSM2246103", "GSM2246104", "GSM2246105", "GSM2246106", "GSM2246107", "GSM2246108", "GSM2246109", "GSM2246110", "GSM2246111", "GSM2246112", "GSM2246113", "GSM2246114", "GSM2246115", "GSM2246116", "GSM2246117", "GSM2246118", "GSM2246119", "GSM2246120", "GSM2246121", "GSM2246122", "GSM2246123", "GSM2246124", "GSM2246125", "GSM2246126", "GSM2246127", "GSM2246128", "GSM2246129", "GSM2246130", "GSM2246131", "GSM2246132", "GSM2246133", "GSM2246134", "GSM2246135", "GSM2246136", "GSM2246137", "GSM2246138", "GSM2246139", "GSM2246140", "GSM2246141", "GSM2246142", "GSM2246143", "GSM2246144", 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migrating front of human glioblastoma", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE84465 not downloaded", "asset:data:geo:GSE84465 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "unsupervised clustering", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Then, we used the R package “Seurat” to perform unsupervised clustering of GBM cells for re-typing and performed a detailed analysis of the biological characteristics of each subtype, including differentially expressed lncRNAs and marker lncRNAs."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (unsupervised clustering), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "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": ["GSE84465"], "resolved_accessions": ["GSE84465"], "statements": ["We downloaded GBM single-cell sequencing data from GSE84465 and performed a series of preprocessing."], "basis": "The paper names GSE84465 in GSE84465 and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33693962", "data:geo:GSE84465"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE84465"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:01:31Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2340, "completion_tokens": 914, "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:33693962", "type": "paper", "label": "pmid:33693962"}, {"id": "source:pmid:33693962", "type": "manuscript", "label": "PMID 33693962 full text"}, {"id": "data:geo:GSE84465", "type": "dataset", "label": "GEO GSE84465"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33693962", "type": "paper", "label": "pmid:33693962"}, {"id": "source:pmid:33693962", "type": "manuscript", "label": "PMID 33693962 full text"}, {"id": "data:geo:GSE84465", "type": "dataset", "label": "GEO GSE84465"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33693962", "type": "extraction", "used": ["source:pmid:33693962"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE84465", "type": "accession_resolution", "used": ["data:geo:GSE84465"], "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:33693962", "parent_hash": "sha256:2eb91dfb7a7fd6abc0ee503dd34022eb807b37880b3243b132798f71b85907c2", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE84465 licence not read", "asset:data:geo:GSE84465 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.99, "evidence": ["is mostly performed based on transcriptome (RNA-seq) without considering lncRNA molecules that a", "olecular typing is mostly performed based on transcriptome (RNA-seq) without considering lncRNA molecul"], "order_basis": "paper_text_order:775", "id": "assay:1"}]},"meta":{"api_version":"v1","automation_ladder_snapshot":"ba34b49490d9bfaf","automation_ladder_caveats":["Method extraction is rule-based and has no hand-judged accuracy sample. Evidence bands order textual support; method agreement intervals are null (n=0), never probabilities. Work-type validation does not validate methods.","Operation coverage describes only explicitly named methods. It does not prove a complete protocol, compatible parameters, successful compilation or re-execution. Unrecognised or ambiguous methods require review.","Data reachability is a textual accession or public-data statement. No dataset was downloaded or checked for access, completeness or licence.","Capabilities are planning states seeded from the dated equipment register. No bench ownership, completed quote or partner booking is inferred. Procurement counts are dependencies, not guaranteed replications or financial returns.","Tier and blocker counts are deterministic assessments of this corpus, not measured agreement. R3 is reserved for procurement; unresolved methods and data require human work (R4). The most restrictive axis wins, with capability, method, data as tie-breaks. Resolving one blocker can leave another at the same tier."],"engine":"corpus_engine","engine_provider":"rule_based_v1+lex99e1195c7d6f","run_id":"run-20261023T122449232913","source":"esearch","source_detail":"PubMed mirror biomed_pubmed (read-only)","run_status":"complete","imported_at":"2026-11-03T20:16:52+00:00","generated_at":"2026-11-04T01:50:34+00:00","total_papers":5529,"total_assays_tracked":29,"automatable_assay_families":6,"validated":true,"caveat_count":9,"blocking_caveats":5,"caveats":[{"code":"low_evidence_dominates","basis":["4,152 of 5,529 classifications (75.1%) matched no cue evidence and sit at the 0.05 floor.","34 of 230 data_only calls (14.8%) are in that group."],"claim":"Work type and confidence bands","gloss":"Most records were classified from their title and framing alone, with assay-cue coverage at zero.","detail":"Most classifications in this run rest on no matched evidence at all. At the evidence floor the work type comes from title framing and a fixed prior, not from anything in the paper, so the published work-type split should be read as a rough triage signal rather than a measured distribution. The impact is bounded but not removed: since 2026-10-23 the engine excludes floor-confidence records from the shortlist entirely and publishes them separately as held out, so the recommendation is unaffected even though the census is.","status":"unverified","severity":"high"},{"code":"runtime_is_modelled","basis":["Runtime is summed from published per-assay hour figures. Timing awaits the first executed replication.","4,407 of 5,529 records (79.7%) model to 0.00 hours because no assay was matched, which the ranking then reads as \"cheapest\".","0 of 10 shortlisted records carry a 0.00-hour estimate."],"claim":"Estimated replication runtime","gloss":"The hour figures are estimates built from assay mentions; timing awaits the first executed replication.","detail":"The hour figures are a cost model derived from the bench steps implied by each matched assay family. The first executed replication will supply measured timing. Records without an assay match currently receive a zero-hour model value.","status":"unverified","severity":"high"},{"code":"signal_score_without_citations","basis":["5,529 of 5,529 records (100.0%) have no citation count from the source metadata."],"claim":"Signal score","gloss":"The signal score uses publication-type weight because the mirror supplied zero citation counts.","detail":"The source supplied no citation counts for any record in this run, so the signal score is publication-type weight only. The citation term of the ranking is inert here, and the shortlist is ordered by publication type alone.","status":"unverified","severity":"high"},{"code":"abstract_absent","basis":["1,667 of 5,529 records (30.2%) carry no abstract at all."],"claim":"Evidence base for classification","gloss":"Some records contain a title and publication type only, defining the available classification evidence.","detail":"Where the mirror contains a title and publication types only, those fields define the classifier evidence. A methods section is required for fuller automated and human review.","status":"unverified","severity":"medium"},{"code":"classifier_agreement_measured","basis":["Published two-way decision agreement 77.7% (310 of 399 decidable records) from a stratified hand-check of 438 real records.","Three-way diagnostic agreement 73.9% (288 of 390 decidable records).","data_only agreement 75.2% (100 of 133 decidable).","48 record(s) could not be decided from title and abstract and were excluded from the denominator.","56 analysis-only records were published under another work type, so the data_only share is not an upper bound."],"claim":"Published automatable decision","gloss":"This figure has been checked against a human reading the same papers, so we know how often it is right.","detail":"The published automatable / not-automatable distribution comes from a rule-based classifier that was hand-checked against a fixed ground-truth definition. The agreement rates below are measured, not estimated. The three-way work type remains a diagnostic and is reported separately.","status":"measured","severity":"high"},{"code":"llm_comparison_not_measured","basis":["rule_based_v1+lex99e1195c7d6f produced 5,529 of 5,529 classifications.","Measured on 438 labelled records; these are RULE-BASED figures, not model results."],"claim":"Rule-based versus LLM agreement","gloss":"Every number here is the rule engine’s own. Model comparison begins when a working API credential is connected and measured.","detail":"The published two-way decision agreed with a human reading on 310 of 399 decidable records (77.7%). The diagnostic three-way label agreed on 288 of 390 decidable records (73.9%). Every percentage in this run belongs to the rule engine. Model comparison begins when a working API credential is connected and measured.","status":"not_measured","severity":"high"},{"code":"confidence_is_a_band","basis":["low band: 135 of 210 hand-judged records were correct, 64.3% [57.6, 70.5] (95% CI).","medium band: 80 of 104 hand-judged records were correct, 76.9% [68.0, 84.0] (95% CI).","high band: 73 of 76 hand-judged records were correct, 96.0% [89.0, 98.7] (95% CI).","A fitted calibrated probability was built, measured and withdrawn: it overstated held-out accuracy and reorders nothing."],"claim":"Confidence band and evidence score","gloss":"The confidence band carries a measured accuracy interval; 0.85 represents relative rank strength.","detail":"Confidence on this run is a BAND plus its measured accuracy interval. The number stored alongside each record is a monotone evidence score that orders records; 0.85 represents relative rank strength. A fitted probability was withdrawn after it overstated held-out accuracy. Threshold on the band.","status":"measured","severity":"medium"},{"code":"three_way_split_is_diagnostic","basis":["The corpus is published at the two-way decision: automatable or not-automatable. The three-way split (data_only / physical / mixed) is published as a diagnostic with its measured reliability attached, not as a claim, because the rule engine's `mixed` call cannot be defended.","The engine called 22 record(s) mixed; 10 matched the human judgement (45.5%, 95% CI 26.9-65.3).","The engine's `mixed` call is right on 10/22 hand-judged records (45.5%, 95% CI 26.9%-65.3%); a constant `physical` guess scores 36.4%.","The engine's `mixed` call does not reliably beat a constant `physical` guess on the hand-judged records it labels mixed.","The sign of that difference flips between two independent samples, so the three-way refinement is not demonstrably informative.","The mixed stratum contributes a disproportionate share of errors relative to its size.","At title-only depth the physical/mixed split collapses: a title says that work was done, not whether it was also analysed."],"claim":"The published decision is two-way","gloss":"The three-way split is shown for diagnosis only. The published split is two ways.","detail":"Count and filter the corpus on automatable versus not-automatable. The data_only / physical / mixed split remains an internal engine diagnostic because the mixed call has lower measured reliability.","status":"measured","severity":"medium"},{"code":"automatable_flag_unproven","basis":["6 of 29 assay families are marked automatable now: meta_analysis, machine_learning, survival_analysis, pca, molecular_docking, differential_expression.","The flag is a rule over assay family and work type; validation begins with the first executed replication.","It inherits the 75.2% data_only agreement rate, because the flag requires the record to be analysis-only."],"claim":"Automatable now","gloss":"This flag marks assay families the rules classify as data-only. The first executed replication will validate it.","detail":"This flag marks families the rules consider replicable from data alone. Its validity depends on the analysis-only classification and will be measured through an executed replication.","status":"unverified","severity":"medium"}],"confidence_policy":"band_with_measured_interval","confidence_contract":{"policy":"band_with_measured_interval","summary":"Confidence is reported as a BAND with a measured accuracy interval. The raw evidence score supplies monotone ordering. A fitted point estimate was withdrawn after it overstated held-out accuracy.","evidence_score":"A monotone evidence score in [0,1] built from cue mass, axis separation and text coverage. Use it to order records. Interpret 0.85 as relative rank strength.","confidence_band":"low | medium | high. Consumers threshold on this value.","band_accuracy":"Wilson 95% interval on the measured agreement of the hand-judged records in this band.","calibrated_confidence":"WITHDRAWN. Reintroduction requires held-out evidence demonstrating reliable estimates across every bin."},"band_accuracy":{"low":{"n":210,"low":0.576,"band":"low","high":0.7046,"agree":135,"accuracy":0.6429},"high":{"n":76,"low":0.8903,"band":"high","high":0.9865,"agree":73,"accuracy":0.9605},"medium":{"n":104,"low":0.6795,"band":"medium","high":0.8397,"agree":80,"accuracy":0.7692}},"provider":"rule_based_v1+lex99e1195c7d6f","lexicon_id":"99e1195c7d6f","contract_published_at":"2026-10-23T12:25:29.022232+00:00","confidence_is_band":true,"confidence_is_probability":false,"decision_taxonomy":"two_way","decidable_fraction_two_way":0.8854,"decidable_fraction_two_way_low":0.8565,"decidable_fraction_two_way_high":0.9143,"decidable_fraction_three_way":0.8586,"decidable_fraction_three_way_low":0.8287,"decidable_fraction_three_way_high":0.8884,"decidable_population":5529,"validation_sample_size":438,"three_way_cost_fraction":0.0268,"three_way_cost_records":148,"decision_counts":{"automatable":230,"not_automatable":5299},"decision_split":{"automatable":{"count":230,"share":0.04159884246699222},"not_automatable":{"count":5299,"share":0.9584011575330078}},"diagnostic_work_type_counts":{"mixed":24,"physical":5275,"data_only":230}}}