Gene signatures with predictive and prognostic survival values in human osteosarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33520450", "kind": "science-record", "revision": 6, "content_hash": "sha256:ce003d7c840e219f7c409fff818b4dd62c4a592acf5536a3e93277a0a20cfbf9", "created_at": "2026-11-01T15:41:23Z", "updated_at": "2026-11-01T21:24:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene signatures with predictive and prognostic survival values in human osteosarcoma.", "doi": "10.7717/peerj.10633", "pmid": "33520450", "authors": ["Zhongpeng Qiu", "Xinhui Du", "Kai Chen", "Yi Dai", "Sibo Wang", "Jun Xiao", "Gang Li"], "journal": "PeerJ", "year": 2021, "abstract": "Osteosarcoma is a common malignancy seen mainly in children and adolescents. The disease is characterized by poor overall prognosis and lower survival due to a lack of predictive markers. Many gene signatures with diagnostic, prognostic, and predictive values were evaluated to achieve better clinical outcomes. Two public data series, GSE21257 and UCSC Xena, were used to identify the minimum number of robust genes needed for a predictive signature to guide prognosis of patients with osteosarcoma. The lasso regression algorithm was used to analyze sequencing data from TCGA-TARGET, and methods such as Cox regression analysis, risk factor scoring, receiving operating curve, KMplot prognosis analysis, and nomogram were used to characterize the prognostic predictive power of the identified genes. Their utility was assessed using the GEO osteosarcoma dataset. Finally, the functional enrichment analysis of the identified genes was performed. A total of twenty-gene signatures were found to have a good prognostic value for predicting patient survival. Gene ontology analysis showed that the key genes related to osteosarcoma were categorized as peptide-antigen binding, clathrin-coated endocytic vesicle membrane, peptide binding, and MHC class II protein complex. The osteosarcoma related genes in these modules were significantly enriched in the processes of antigen processing and presentation, phagocytosis, cell adhesion molecules, Staphylococcus aureus infection. Twenty gene signatures were identified related to osteosarcoma, which would be helpful for predicting prognosis of patients with OS. Further, these signatures can be used to determine the subtypes of osteosarcoma.", "claims": [{"id": "claim-method", "statement": "The method chosen by lasso Cox was 10-fold cross-validation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33520450", "locator": "sections[4] \"Construction of gene signatures\" paragraph 2", "quote": "The method chosen by lasso Cox was 10-fold cross-validation."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33520450", "locator": "sections[25] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files."}], "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:33520450"], "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:GSE21257"], "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:GSE21257"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33520450", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.10633", "sha256": "sha256:a7f9c82dd111434ae194b0d618531e61af6581a2a78c37f071d6998b8e52f3e6", "bytes": 42680, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.10633", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7812922", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE21257", "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=GSE21257", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE21257", "version": null, "note": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM530667", "GSM530899", "GSM531283", "GSM531284", "GSM531285", "GSM531286", "GSM531287", "GSM531288", "GSM531289", "GSM531290", "GSM531291", "GSM531292", "GSM531293", "GSM531294", "GSM531295", "GSM531296", "GSM531297", "GSM531298", "GSM531299", "GSM531300", "GSM531301", "GSM531302", "GSM531303", "GSM531304", "GSM531305", "GSM531306", "GSM531307", "GSM531308", "GSM531309", "GSM531310", "GSM531311", "GSM531312", "GSM531313", "GSM531314", "GSM531319", "GSM531320", "GSM531321", "GSM531322", "GSM531323", "GSM531324", "GSM531325", "GSM531326", "GSM531327", "GSM531328", "GSM531329", "GSM531330", "GSM531331", "GSM531332", "GSM531333", "GSM531334", "GSM531335", "GSM531351", "GSM531352"], "sample_count": 53, "group_sizes": null, "group_sizes_basis": null, "platform": "10295", "taxon": "Homo sapiens", "title": "Genome-wide gene expression profiling on pre-chemotherapy biopsies of osteosarcoma patients who developed metastases within 5yrs (n=34) and patients who did not develop metastases within 5yrs (n=19)", "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:33520450:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:c252dcb48d671318d615a0d81cfaa9a1f9115add640bb5a92ec4c052abc3061a", "bytes": 2251, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[1]/table-wrap[1]#table-1", "version": null, "note": "Potential biomarkers for osteosarcoma.", "structure": {"pmcid": "PMC7812922", "section_index": 1, "section_title": "Introduction", "row_count": 18, "column_count": 7}, "table": {"label": "Table 1", "caption": "Potential biomarkers for osteosarcoma.", "rows": [["Study approach", "Type of biomarker", "Candidate biomarker", "Regulation", "Sample", "Technique", "Reference"], ["Genomics", "Diagnostic", "C7orf24", "↑", "Tissue; cell lines", "RT-PCR; qRT-PCR; Western blot (WB); siRNA transfection", "Uejima et al. (2011)"], ["Diagnostic And Predictive", "miRNA signatures", "−", "Tissue; cell lines", "qRT-PCR", "Gougelet et al. (2011)"], ["Predictive", "Multigene classifier", "−", "Tissue", "cDNA microarray; qRT-PCR", "Man et al. (2005)"], ["Predictive", "Multigene classifier", "−", "Tissue", "cDNA microarray; RT-PC", "Mintz et al. (2005)"], ["Predictive And Prognosis", "miRNA signatures", "−", "Tissue", "miRNA microarray; qRT-PCR; immunohistochemistry (IHC)", "Jones et al. (2012)"], ["Predictive And Prognosis", "miR-21", "↑", "Serum", "qRT-PCR", "Yuan et al. (2012)"], ["Prognosis", "Tenascin-C", "↓", "Cell lines", "cDNA microarray; RT-PCR; WB; IHC", "Xiong et al. (2009)"], ["Prognostic", "miRNA-214", "↑", "Tissue", "qRT-PCR", "Wang et al. (2014)"], ["Proteomics", "Diagnostic", "Serum amyloid A (SAA)", "↑", "Plasma", "SELDI-TOF MS; WB", "Li et al. (2010)"], ["Diagnostic", "Ezrin (EZR); a crystallin β chain (CRYAB)", "↑", "Tissue", "2D-DIGE; LC-ESI-MS/MS; RT-PCR for mRNA; tissue microarray and IHC", "Folio et al. (2009)"], ["Diagnostic", "Cytochrome C1 (CYC-1)", "↑", "Serum; cell lines", "SELDI-TOF MS; Gene microarray (cell lines)", "Li et al. (2009)"], ["Diagnostic", "Zinc finger protein 133 (ZNF 133); tubulin-a1c (TUBA1C)", "↑", "Tissue", "2-DE; MALDI-TOF MS; WB; IHC", "Li et al. (2010)"], ["Diagnostic", "Protein NDRG 1", "↑", "Plasma membrane from cell line and tissue", "2-DE; LC-ESI-MS/MS; IHC; WB", "Hua et al. (2011)"], ["Diagnostic", "Gelsolin", "↓", "Serum", "2D-DIGE; MALDIHTOF; WB; ELISA", "Jin et al. (2012)"], ["Predictive And Prognostic", "SAA", "↑", "Serum", "2D-DIGE; MALDI-TOF MS; WB; ELISA", "Jin et al. (2007)"], ["Predictive", "Peroxiredoxin 2 (PRDX2)", "↑(poor prognosis)", "Tissue", "2D-DIGE; LC-ESI-MS/MS; WB", "Kikuta et al. (2010)"], ["Predictive", "SAA; transthyretin (TTR)", "↑(poor prognosis)", "Plasma", "SELDI-TOF MS; WB", "Li et al. (2011)"]], "row_count": 18, "column_count": 7, "numeric_cells": 30, "header_rows": 1, "locator": "section[1]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:33520450:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7012df299348deed48055a39b9e1e9f3a6015cfd10eaaf2c73dca19364b5dbc0", "bytes": 2380, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#table-2", "version": null, "note": "Twenty genes significantly related to the overall survival in the training set underlying the LASSO model.", "structure": {"pmcid": "PMC7812922", "section_index": 9, "section_title": "Construction of genes classifier for OS", "row_count": 21, "column_count": 6}, "table": {"label": "Table 2", "caption": "Twenty genes significantly related to the overall survival in the training set underlying the LASSO model.", "rows": [["Ensemble ID", "Gene", "Chromosome location", "Coefficient of lasso model", "HR", "p value"], ["ENSG00000103274.9", "NUBP1", "chr16:10743786-10769351:(+)", "−0.2216", "0.905 (0.86, 0.953)", "0.000"], ["ENSG00000163219.10", "ARHGAP25", "chr2:68679601-68826833:(+)", "−0.0503", "0.795 (0.685, 0.924)", "0.003"], ["ENSG00000077420.14", "APBB1IP", "chr10:26438203-26567803:(+)", "−0.0429", "0.924 (0.88, 0.97)", "0.001"], ["ENSG00000162517.11", "PEF1", "chr1:31629862-31644896:(-)", "−0.0230", "0.979 (0.966, 0.992)", "0.002"], ["ENSG00000102226.8", "USP11", "chrX:47232690-47248328:(+)", "−0.0123", "0.982 (0.97, 0.994)", "0.004"], ["ENSG00000179163.11", "FUCA1", "chr1:23845077-23868294:(-)", "−0.0104", "0.969 (0.949, 0.99)", "0.003"], ["ENSG00000189171.12", "S100A13", "chr1:153618787-153634092:(-)", "0.0019", "1.007 (1.004, 1.011)", "0.000"], ["ENSG00000132535.17", "DLG4", "chr17:7189890-7219702:(-)", "0.0088", "1.064 (1.021, 1.109)", "0.003"], ["ENSG00000158315.9", "RHBDL2", "chr1:38885807-38941799:(-)", "0.0144", "1.01 (1.006, 1.013)", "0.000"], ["ENSG00000176171.10", "BNIP3", "chr10:131966455-131981931:(-)", "0.0170", "1.009 (1.004, 1.014)", "0.000"], ["ENSG00000167549.17", "CORO6", "chr17:29614756-29622907:(-)", "0.0425", "1.054 (1.021, 1.088)", "0.001"], ["ENSG00000125337.15", "KIF25", "chr6:167996241-168045089:(+)", "0.0570", "1.148 (1.076, 1.224)", "0.000"], ["ENSG00000179262.8", "RAD23A", "chr19:12945855-12953642:(+)", "0.0741", "1.005 (1.002, 1.008)", "0.000"], ["ENSG00000147378.10", "FATE1", "chrX:151716035-151723194:(+)", "0.0862", "2.217 (1.518, 3.238)", "0.000"], ["ENSG00000113739.9", "STC2", "chr5:173314713-173329503:(-)", "0.0895", "1.016 (1.005, 1.027)", "0.004"], ["ENSG00000197467.12", "COL13A1", "chr10:69801931-69964275:(+)", "0.0910", "1.021 (1.013, 1.029)", "0.000"], ["ENSG00000017483.13", "SLC38A5", "chrX:48458537-48470256:(-)", "0.1003", "1.008 (1.003, 1.014)", "0.002"], ["ENSG00000136997.13", "MYC", "chr8:127735434-127741434:(+)", "0.1635", "1.003 (1.002, 1.005)", "0.000"], ["ENSG00000138028.13", "CGREF1", "chr2:27098889-27119115:(-)", "0.2105", "1.015 (1.009, 1.021)", "0.000"], ["ENSG00000241563.3", "CORT", "chr1:10449719-10451902:(+)", "0.2504", "1.026 (1.016, 1.036)", "0.000"]], "row_count": 21, "column_count": 6, "numeric_cells": 107, "header_rows": 1, "locator": "section[9]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:33520450:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4dfd6875d2db9cf42459ecc76dda04ac6bf5a71f82f366b1fb46bba0c1ba022d", "bytes": 831, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#table-3", "version": null, "note": "Univariate and multivariate Cox regression analyses genes signiture for patients with osteosarcoma in study cohort.", "structure": {"pmcid": "PMC7812922", "section_index": 11, "section_title": "Validation of twenty-gene signature for survival prediction in the validation set", "row_count": 8, "column_count": 5}, "table": {"label": "Table 3", "caption": "Univariate and multivariate Cox regression analyses genes signiture for patients with osteosarcoma in study cohort.", "rows": [["", "Univariate", "Multivariate"], ["Characteristics", "HR", "p.value", "HR", "p.value"], ["Gender (Female vs Male)", "0.666 (0.317, 1.399)", "0.283", "", ""], ["Age (<18 vs ≥18)", "0.909 (0.345, 2.393)", "0.846", "", ""], ["Recurrence (No vs Yes)", "19.348 (4.589, 81.563)", "<0.001", "5.374 (1.183, 24.404)", "0.029"], ["Primary tumor site (Arm/Hand OR Pelvis vs Leg/Foot)", "0.487 (0.168, 1.413)", "0.185", "", ""], ["Specific tumor site (Femur vs Tibia or others)", "0.642 (0.309, 1.337)", "0.236", "", ""], ["riskscore", "13.915 (7.067, 27.398)", "<0.001", "9.869 (4.663, 20.887)", "<0.001"]], "row_count": 8, "column_count": 5, "numeric_cells": 17, "header_rows": 2, "locator": "section[11]/table-wrap[1]#table-3"}}, {"id": "asset:table:pmid:33520450:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:04af164a4b2c95a6308e5f4946cf20906cc783d680e22cef809b659f157d9ac9", "bytes": 1122, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[12]/table-wrap[1]#table-4", "version": null, "note": "Relationship between risk score of the 20-marker-based prognostic classifier with os and clinical characteristics in the training set.", "structure": {"pmcid": "PMC7812922", "section_index": 12, "section_title": "Gene co-expression network analysis", "row_count": 16, "column_count": 5}, "table": {"label": "Table 4", "caption": "Relationship between risk score of the 20-marker-based prognostic classifier with os and clinical characteristics in the training set.", "rows": [["Characters", "Level", "Low risk", "High risk", "P value"], ["n", "", "42", "42", ""], ["Gender", "Female (%)", "16 ( 38.1)", "21 (50.0)", "0.379"], ["", "Male (%)", "26 ( 61.9)", "21 (50.0)", ""], ["Age", "<18 (%)", "32 ( 76.2)", "34 (81.0)", "0.791"], ["", "≥18 (%)", "10 ( 23.8)", "8 (19.0)", ""], ["Overall survival", "Alived (%)", "42 (100.0)", "13 (31.0)", "<0.001"], ["", "Dead (%)", "0 ( 0.0)", "29 (69.0)", ""], ["Recurrence", "No (%)", "32 ( 76.2)", "13 (31.0)", "<0.001"], ["", "Yes (%)", "10 ( 23.8)", "29 (69.0)", ""], ["Metastasis", "No (%)", "37 ( 88.1)", "26 (61.9)", "0.011"], ["", "Yes (%)", "5 ( 11.9)", "16 (38.1)", ""], ["Primary tumor site", "Arm/Hand OR Pelvis (%)", "3 ( 7.1)", "5 (11.9)", "0.713"], ["", "Leg/Foot (%)", "39 ( 92.9)", "37 (88.1)", ""], ["Specific tumor site", "Femur (%)", "13 ( 31.0)", "25 (59.5)", "0.015"], ["", "Tibia or others (%)", "29 ( 69.0)", "17 (40.5)", ""]], "row_count": 16, "column_count": 5, "numeric_cells": 39, "header_rows": 1, "locator": "section[12]/table-wrap[1]#table-4"}}], "gaps": ["asset:data:geo:GSE21257 not downloaded", "asset:data:geo:GSE21257 licence not read"]}, "analysis": {"state": "complete", "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": "The method chosen by lasso Cox was 10-fold cross-validation."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "KM"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-4", "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": "dendrogram"}}, {"id": "method-5", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}], "targets": [], "gaps": []}, "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": ["GSE21257"], "resolved_accessions": ["GSE21257"], "statements": ["The following information was supplied regarding data availability:\nThe raw measurements are available in the Supplemental Files."], "basis": "The paper names GSE21257 in GEO database 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:33520450", "data:geo:GSE21257", "asset:table:pmid:33520450:1", "asset:table:pmid:33520450:2", "asset:table:pmid:33520450:3", "asset:table:pmid:33520450:4"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE21257"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:26:30Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34395, "completion_tokens": 1213, "cached_tokens": 792}}, "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:33520450", "type": "paper", "label": "pmid:33520450"}, {"id": "source:pmid:33520450", "type": "manuscript", "label": "PMID 33520450 full text"}, {"id": "data:geo:GSE21257", "type": "dataset", "label": "GEO GSE21257"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33520450", "type": "paper", "label": "pmid:33520450"}, {"id": "source:pmid:33520450", "type": "manuscript", "label": "PMID 33520450 full text"}, {"id": "data:geo:GSE21257", "type": "dataset", "label": "GEO GSE21257"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33520450", "type": "extraction", "used": ["source:pmid:33520450"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE21257", "type": "accession_resolution", "used": ["data:geo:GSE21257"], "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:33520450", "parent_hash": "sha256:d99a70e7c5de1ee95967f3257e7606e13dfb3ce4433ea9f7826d630429bd59b1", "fork_of": null, "generation": 5}, "gaps": ["asset:data:geo:GSE21257 licence not read", "asset:data:geo:GSE21257 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["The method chosen by lasso Cox was 10-fold cross-validation."], "order_basis": "analysis_only", "id": "assay:1"}]}