{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29379305", "kind": "science-record", "revision": 8, "content_hash": "sha256:06cbf9223e9e80e0e6c6aa57fec5dd3cb8efb671a75c7c677eb93dd86d5ea092", "created_at": "2026-11-01T15:40:31Z", "updated_at": "2026-11-01T21:59:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A support vector machine and a random forest classifier indicates a 15-miRNA set related to osteosarcoma recurrence.", "doi": "10.2147/OTT.S148394", "pmid": "29379305", "authors": ["Yunfei He", "Jun Ma", "An Wang", "Weiheng Wang", "Shengchang Luo", "Yaoming Liu", "Xiaojian Ye"], "journal": "OncoTargets and therapy", "year": 2018, "abstract": "BACKGROUND: Osteosarcoma, which originates in the mesenchymal tissue, is the prevalent primary solid malignancy of the bone. It is of great importance to explore the mechanisms of metastasis and recurrence, which are two primary reasons accounting for the high death rate in osteosarcoma.\nDATA AND METHODS: Three miRNA expression profiles related to osteosarcoma were downloaded from GEO DataSets. Differentially expressed miRNAs (DEmiRs) were screened using MetaDE.ES of the MetaDE package. A support vector machine (SVM) classifier was constructed using optimal miRNAs, and its prediction efficiency for recurrence was detected in independent datasets. Finally, a co-expression network was constructed based on the DEmiRs and their target genes.\nRESULTS: In total, 78 significantly DEmiRs were screened. The SVM classifier constructed by 15 miRNAs could accurately classify 58 samples in 65 samples (89.2%) in the GSE39040 database, which was validated in another two databases, GSE39052 (84.62%, 22/26) and GSE79181 (91.3%, 21/23). Cox regression showed that four miRNAs, including hsa-miR-10b, hsa-miR-1227, hsa-miR-146b-3p, and hsa-miR-873, significantly correlated with tumor recurrence time. There were 137, 147, 145, and 77 target genes of the above four miRNAs, respectively, which were assigned to 17 gene ontology functionally annotated terms and 14 Kyoto Encyclopedia of Genes and Genomes pathways. Among them, the \"Osteoclast differentiation\" pathway contained a total of seven target genes and was analyzed further.\nCONCLUSION: The 15-miRNAs-based SVM classifier provides a potential useful tool to predict the recurrence of osteosarcoma. Our results suggest the possible mechanisms of osteosarcoma metastasis and recurrence and provide fresh DEmiRs as potential biomarkers or therapeutic targets for osteosarcoma.", "claims": [{"id": "claim-method", "statement": "With expression values of the optimal feature combination of miRNAs as variables, associations of optimal feature miRNAs with recurrence time were studied by Cox regression analysis using the coxph R function of the survival package in R language.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29379305", "locator": "sections[12] \"Cox regression analysis of optimal feature miRNAs and recurrence time\" paragraph 2", "quote": "With expression values of the optimal feature combination of miRNAs as variables, associations of optimal feature miRNAs with recurrence time were studied by Cox regression analysis using the coxph R function of the survival package in R language."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Three miRNA expression profiles, named GSE39040, GSE39052, and GSE79181, were achieved, among which the former two emerged from the platform “GPL15762 Illumina Human v2 MicroRNA Expression BeadChip”, whereas the last one arose from the platform “GPL15497 Applied Biosystems TaqMan Array Human MicroRNA Cards”. There were 23, 15, and 14 osteosarcoma recurrence samples, and 42, 11, and 9 osteosarcoma non-recurrence samples in these three datasets, separately.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29379305", "locator": "sections[3] \"Collection and pretreatment of expression profile data\" paragraph 2", "quote": "Three miRNA expression profiles, named GSE39040, GSE39052, and GSE79181, were achieved, among which the former two emerged from the platform “GPL15762 Illumina Human v2 MicroRNA Expression BeadChip”, whereas the last one arose from the platform “GPL15497 Applied Biosystems TaqMan Array Human MicroRNA Cards”. There were 23, 15, and 14 osteosarcoma recurrence samples, and 42, 11, and 9 osteosarcoma non-recurrence samples in these three datasets, separately."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Using MetaDE.ES to screen differentially expressed miRNAs from three GEO DataSets and an SVM classifier trained on 15 selected miRNAs in GSE39040, the study accurately classified 58 of 65 samples in GSE39040 (89.2%) and achieved 84.62% accuracy in GSE39052 and 91.3% in GSE79181.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29379305", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Three miRNA expression profiles related to osteosarcoma were downloaded from GEO DataSets. Differentially expressed miRNAs (DEmiRs) were screened using MetaDE.ES of the MetaDE package. A support vector machine (SVM) classifier was constructed using optimal miRNAs, and its prediction efficiency for recurrence was detected in independent datasets."}, {"asset": "source:pmid:29379305", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The SVM classifier constructed by 15 miRNAs could accurately classify 58 samples in 65 samples (89.2%) in the GSE39040 database, which was validated in another two databases, GSE39052 (84.62%, 22/26) and GSE79181 (91.3%, 21/23)."}, {"asset": "source:pmid:29379305", "locator": "sections[22] \"Independent validation and evaluation of SVM classifier performance\" paragraph 2", "quote": "The results showed that the SVM classifier categorized 22 samples precisely in GSE39052, with a classification accuracy rate of 84.62% (22/26); 21 of 23 samples were accurately classified in GSE79181, with 91.3% accuracy rate."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Using MetaDE.ES to screen differentially expressed miRNAs from three GEO DataSets and an SVM classifier trained on 15 selected miRNAs in GSE39040, the study accurately classified 58 of 65 samples in GSE39040 (89.2%) and achieved 84.62% accuracy in GSE39052 and 91.3% in GSE79181.", "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:29379305"], "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:GSE39040"], "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:GSE39040"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29379305", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S148394", "sha256": "sha256:1edee76e8d178e316b79c944e4cda2195dd0a6be9012da1a3af32a5205585f6e", "bytes": 57689, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S148394", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5759858", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE39040", "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=GSE39040", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39040", "version": null, "note": "Three miRNA expression profiles, named GSE39040, GSE39052, and GSE79181, were achieved, among which the former two emerged from the platform “GPL15762 Illumina Human v2 MicroRNA Expression BeadChip”, whereas the last one arose from the platform “GPL15497 Applied Biosystems TaqMan Array Human MicroRNA Cards”. 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differential expression", "structure": {"pmcid": "PMC5759858", "section_index": 29, "section_title": "Supplementary materials", "row_count": 79, "column_count": 5}, "table": {"label": "Table S1", "caption": "Screened 78 miRNAs with significant differential expression", "rows": [["miRNA_ID", "P-value", "Q", "Qp", "tau2"], ["hsa-miR-432", "0.00002", "0.6704", "0.7152", "0"], ["hsa-miR-329", "0.00002", "0.2139", "0.8986", "0"], ["hsa-miR-889", "0.0002", "0.7548", "0.6857", "0"], ["hsa-miR-337-3p", "0.0002", "0.0778", "0.9619", "0"], ["hsa-miR-635", "0.0004", "0.4406", "0.8023", "0"], ["hsa-miR-296-3p", "0.0004", "1.4533", "0.4835", "0"], ["hsa-miR-548c-3p", "0.0006", "0.8417", "0.6565", "0"], ["hsa-miR-625", "0.0006", "0.0724", "0.9644", "0"], ["hsa-miR-551a", "0.0006", "0.2312", "0.8908", "0"], ["hsa-miR-510", "0.0006", "0.0666", "0.9672", "0"], ["hsa-miR-10b", "0.0009", "1.6776", "0.4322", "0"], ["hsa-miR-375", "0.0015", "1.2804", "0.5272", "0"], ["hsa-miR-586", "0.0017", "0.1737", 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"0.0122", "0.2137", "0.8987", "0"], ["hsa-miR-409-3p", "0.0124", "0.3380", "0.8445", "0"], ["hsa-miR-362-3p", "0.0128", "1.5226", "0.4671", "0"], ["hsa-miR-520a-3p", "0.0129", "1.0973", "0.5777", "0"], ["hsa-miR-299-5p", "0.0141", "0.9906", "0.6094", "0"], ["hsa-miR-99b", "0.0145", "1.2373", "0.5387", "0"], ["hsa-miR-576-3p", "0.0198", "1.0569", "0.5895", "0"], ["hsa-miR-636", "0.0202", "0.9612", "0.6184", "0"], ["hsa-miR-31", "0.0207", "1.4158", "0.4927", "0"], ["hsa-miR-543", "0.0219", "0.0557", "0.9725", "0"], ["hsa-miR-509-5p", "0.0233", "0.2104", "0.9002", "0"], ["hsa-miR-873", "0.0237", "0.1581", "0.9240", "0"], ["hsa-miR-572", "0.0245", "0.2224", "0.8947", "0"], ["hsa-miR-148b", "0.0251", "1.7011", "0.4272", "0"], ["hsa-miR-324-5p", "0.0262", "1.6948", "0.4285", "0"], ["hsa-miR-422a", "0.0262", "0.3929", "0.8217", "0"], ["hsa-miR-181a", "0.0269", "0.5740", "0.7505", "0"], ["hsa-miR-25", "0.0276", "1.7530", "0.4162", "0"], ["hsa-miR-29c", "0.0286", "0.3219", "0.8513", "0"], ["hsa-miR-517c", "0.0290", "0.7942", "0.6723", "0"], ["hsa-miR-501-5p", "0.0296", "0.7887", "0.6741", "0"], ["hsa-miR-639", "0.0296", "0.6441", "0.7247", "0"], ["hsa-miR-1275", "0.0296", "0.2700", "0.8737", "0"], ["hsa-miR-129-3p", "0.0326", "0.6742", "0.7138", "0"], ["hsa-miR-921", "0.0327", "0.3280", "0.8487", "0"], ["hsa-miR-124", "0.0338", "0.7222", "0.6969", "0"], ["hsa-miR-147", "0.0358", "0.4122", "0.8138", "0"], ["hsa-miR-28-5p", "0.0362", "0.4770", "0.7878", "0"], ["hsa-miR-200c", "0.0365", "0.9670", "0.6166", "0"], ["hsa-miR-518f", "0.0382", "1.0540", "0.5904", "0"], ["hsa-miR-134", "0.0390", "1.2245", "0.5421", "0"], ["hsa-miR-29a", "0.0395", "0.4061", "0.8162", "0"], ["hsa-miR-337-5p", "0.0399", "0.9856", "0.6109", "0"], ["hsa-miR-501-3p", "0.0402", "1.0533", "0.5906", "0"], ["hsa-miR-139-3p", "0.0407", "1.7569", "0.4154", "0"], ["hsa-miR-122", "0.0425", "0.0150", "0.9925", "0"], ["hsa-miR-431", "0.0425", "0.0928", "0.9546", "0"], ["hsa-miR-630", "0.0436", "0.8171", "0.6646", "0"], ["hsa-miR-1227", "0.0437", "0.4731", "0.7894", "0"], ["hsa-miR-136", "0.0441", "0.4049", "0.8167", "0"], ["hsa-miR-127-3p", "0.0470", "0.2269", "0.8928", "0"], ["hsa-miR-204", "0.0471", "0.1403", "0.9322", "0"], ["hsa-miR-361-3p", "0.0471", "0.5252", "0.7691", "0"], ["hsa-miR-720", "0.0488", "0.1208", "0.9414", "0"], ["hsa-miR-342-5p", "0.0490", "0.5989", "0.7412", "0"], ["hsa-miR-885-3p", "0.0494", "0.8097", "0.6671", "0"], ["hsa-miR-302d", "0.0497", "0.5082", "0.7756", "0"]], "row_count": 79, "column_count": 5, "numeric_cells": 390, "header_rows": 1, "locator": "section[29]/table-wrap[1]#ts1-ott-11-253"}}, {"id": "asset:table:pmid:29379305:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2bbe94df371cc98814666f09e6f4bc7c8d7abcfd537ada39d2c9186354d97058", "bytes": 1801, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": 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PRKAB2, GTF2H4, MAP3K7, RB1CC1"]], "row_count": 18, "column_count": 4, "numeric_cells": 40, "header_rows": 1, "locator": "section[29]/table-wrap[2]#ts2-ott-11-253"}}, {"id": "asset:table:pmid:29379305:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:15f52b4200e606f5e503de2593295e54ceba840e66983b7d278226afe0581458", "bytes": 1298, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[29]/table-wrap[3]#ts3-ott-11-253", "version": null, "note": "The KEGG pathway significantly related to target genes", "structure": {"pmcid": "PMC5759858", "section_index": 29, "section_title": "Supplementary materials", "row_count": 15, "column_count": 4}, "table": {"label": "Table S3", "caption": "The KEGG pathway significantly related to target genes", "rows": [["Term", "Count", "P-value", "Genes"], ["Arginine biosynthesis", "3", "0.0100", "ARG2, GOT2, GLS"], ["Fatty acid elongation", "3", "0.0171", "ELOVL2, ELOVL4, ELOVL6"], ["Nucleotide excision repair", "4", "0.0178", "GTF2H1, LIG1, RAD23B, GTF2H4"], ["Osteoclast differentiation", "7", "0.0195", "IL1A, CAMK4, TNFSF11, NCF4, PPP3CB, MAP3K7, SOCS3"], ["Rheumatoid arthritis", "5", "0.0379", "ITGAL, TNFSF11, IL8, MMP3, IL1A"], ["Phenylalanine metabolism", "2", "0.0128", "GLYAT, GOT2"], ["Selenocompound metabolism", "2", "0.0128", "SEPHS1, TXNRD1"], ["Fat digestion and absorption", "3", "0.0152", "PNLIPRP1, ABCA1, GOT2"], ["Ubiquitin-mediated proteolysis", "6", "0.0235", "PIAS3, CBL, TRIM32, ITCH, TRIM37, SOCS3"], ["Biosynthesis of amino acids", "4", "0.0276", "ARG2, GOT2, RPE, MAT2B"], ["Transcriptional misregulation in cancer", "7", "0.0351", "CDK9, MMP3, IL8, PAX5, RXRB, CCNA1, DDX5"], ["RNA degradation", "4", "0.0354", "DDX6, CNOT6, 10200, CNOT4"], ["Biosynthesis of unsaturated fatty acids", "2", "0.0459", "ELOVL2, ELOVL6"], ["Non-alcoholic fatty liver disease (NAFLD)", "6", "0.0500", "IL1A, PRKAB2, IL8, ITCH, NDUFA4L2, SOCS3"]], "row_count": 15, "column_count": 4, "numeric_cells": 33, "header_rows": 1, "locator": "section[29]/table-wrap[3]#ts3-ott-11-253"}}, {"id": "asset:table:pmid:29379305:7", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6870e71d0603b192eb924f1eef2a4d8a3cac4457b1cc4335ec57cbef6421d8ca", "bytes": 4036, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[34]/table-wrap[1]#db_ds_table-wrap1_reqid_", "version": null, "note": "Screened 78 miRNAs with significant differential expression", "structure": {"pmcid": "PMC5759858", "section_index": 34, "section_title": "Supplementary Materials", "row_count": 79, "column_count": 5}, "table": {"label": "Table S1", "caption": "Screened 78 miRNAs with significant differential expression", "rows": [["miRNA_ID", "P-value", "Q", "Qp", "tau2"], ["hsa-miR-432", "0.00002", "0.6704", "0.7152", "0"], ["hsa-miR-329", "0.00002", "0.2139", "0.8986", "0"], ["hsa-miR-889", "0.0002", "0.7548", "0.6857", "0"], ["hsa-miR-337-3p", "0.0002", "0.0778", "0.9619", "0"], ["hsa-miR-635", "0.0004", "0.4406", "0.8023", "0"], ["hsa-miR-296-3p", "0.0004", "1.4533", "0.4835", "0"], ["hsa-miR-548c-3p", "0.0006", "0.8417", "0.6565", "0"], ["hsa-miR-625", "0.0006", "0.0724", "0.9644", "0"], ["hsa-miR-551a", "0.0006", "0.2312", "0.8908", "0"], ["hsa-miR-510", "0.0006", "0.0666", "0.9672", "0"], ["hsa-miR-10b", "0.0009", "1.6776", "0.4322", "0"], ["hsa-miR-375", "0.0015", "1.2804", "0.5272", "0"], ["hsa-miR-586", "0.0017", "0.1737", "0.9168", "0"], ["hsa-miR-211", "0.0018", "1.2030", "0.5480", "0"], ["hsa-miR-338-3p", "0.0030", "0.3902", "0.8227", "0"], ["hsa-miR-509-3-5p", "0.0030", "0.5238", "0.7696", "0"], ["hsa-miR-601", "0.0032", "0.8572", "0.6514", "0"], ["hsa-miR-506", "0.0035", "0.1168", "0.9433", "0"], ["hsa-miR-493", "0.0036", "0.8930", "0.6399", "0"], ["hsa-miR-382", "0.0052", "0.4549", "0.7966", "0"], ["hsa-miR-448", "0.0052", "0.3315", "0.8473", "0"], ["hsa-miR-485-3p", "0.0056", "1.9759", "0.3723", "0"], ["hsa-miR-330-3p", "0.0061", "1.7235", "0.4224", "0"], ["hsa-miR-885-5p", "0.0062", "0.4348", "0.8046", "0"], ["hsa-miR-154", "0.0067", "0.5234", "0.7697", "0"], ["hsa-miR-323-3p", "0.0073", "1.4660", "0.4805", "0"], ["hsa-miR-381", "0.0081", "1.0856", "0.5811", "0"], ["hsa-miR-146b-3p", "0.0083", "0.1552", "0.9253", "0"], ["hsa-miR-1324", "0.0092", "0.2516", "0.8818", "0"], ["hsa-miR-544", "0.0095", "0.2217", "0.8951", "0"], ["hsa-miR-342-3p", "0.0099", "1.7962", "0.4073", "0"], ["hsa-miR-944", "0.0122", "0.2137", "0.8987", "0"], ["hsa-miR-409-3p", "0.0124", "0.3380", "0.8445", "0"], ["hsa-miR-362-3p", "0.0128", "1.5226", "0.4671", "0"], ["hsa-miR-520a-3p", "0.0129", "1.0973", "0.5777", "0"], ["hsa-miR-299-5p", "0.0141", "0.9906", "0.6094", "0"], ["hsa-miR-99b", "0.0145", "1.2373", "0.5387", "0"], ["hsa-miR-576-3p", "0.0198", "1.0569", "0.5895", "0"], ["hsa-miR-636", "0.0202", "0.9612", "0.6184", "0"], ["hsa-miR-31", "0.0207", "1.4158", "0.4927", "0"], ["hsa-miR-543", "0.0219", "0.0557", "0.9725", "0"], ["hsa-miR-509-5p", "0.0233", "0.2104", "0.9002", "0"], ["hsa-miR-873", "0.0237", "0.1581", "0.9240", "0"], ["hsa-miR-572", "0.0245", "0.2224", "0.8947", "0"], ["hsa-miR-148b", "0.0251", "1.7011", "0.4272", "0"], ["hsa-miR-324-5p", "0.0262", "1.6948", "0.4285", "0"], ["hsa-miR-422a", "0.0262", "0.3929", "0.8217", "0"], ["hsa-miR-181a", "0.0269", "0.5740", "0.7505", "0"], ["hsa-miR-25", "0.0276", "1.7530", "0.4162", "0"], ["hsa-miR-29c", "0.0286", "0.3219", "0.8513", "0"], ["hsa-miR-517c", "0.0290", "0.7942", "0.6723", "0"], ["hsa-miR-501-5p", "0.0296", "0.7887", "0.6741", "0"], ["hsa-miR-639", "0.0296", "0.6441", "0.7247", "0"], ["hsa-miR-1275", "0.0296", "0.2700", "0.8737", "0"], ["hsa-miR-129-3p", "0.0326", "0.6742", "0.7138", "0"], ["hsa-miR-921", "0.0327", "0.3280", "0.8487", "0"], ["hsa-miR-124", "0.0338", "0.7222", "0.6969", "0"], ["hsa-miR-147", "0.0358", "0.4122", "0.8138", "0"], ["hsa-miR-28-5p", "0.0362", "0.4770", "0.7878", "0"], ["hsa-miR-200c", "0.0365", "0.9670", "0.6166", "0"], ["hsa-miR-518f", "0.0382", "1.0540", "0.5904", "0"], ["hsa-miR-134", "0.0390", "1.2245", "0.5421", "0"], ["hsa-miR-29a", "0.0395", "0.4061", "0.8162", "0"], ["hsa-miR-337-5p", "0.0399", "0.9856", "0.6109", "0"], ["hsa-miR-501-3p", "0.0402", "1.0533", "0.5906", "0"], ["hsa-miR-139-3p", "0.0407", "1.7569", "0.4154", "0"], ["hsa-miR-122", "0.0425", "0.0150", "0.9925", "0"], ["hsa-miR-431", "0.0425", "0.0928", "0.9546", "0"], ["hsa-miR-630", "0.0436", "0.8171", "0.6646", "0"], ["hsa-miR-1227", "0.0437", "0.4731", "0.7894", "0"], ["hsa-miR-136", "0.0441", "0.4049", "0.8167", "0"], ["hsa-miR-127-3p", "0.0470", "0.2269", "0.8928", "0"], ["hsa-miR-204", "0.0471", "0.1403", "0.9322", "0"], ["hsa-miR-361-3p", "0.0471", "0.5252", "0.7691", "0"], ["hsa-miR-720", "0.0488", "0.1208", "0.9414", "0"], ["hsa-miR-342-5p", "0.0490", "0.5989", "0.7412", "0"], ["hsa-miR-885-3p", "0.0494", "0.8097", "0.6671", "0"], ["hsa-miR-302d", "0.0497", "0.5082", "0.7756", "0"]], "row_count": 79, "column_count": 5, "numeric_cells": 390, "header_rows": 1, "locator": "section[34]/table-wrap[1]#db_ds_table-wrap1_reqid_"}}, {"id": "asset:table:pmid:29379305:8", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:59fededcdd919295607e8d8e146e84c2c974402960b30a55d37a4c1caa716bee", "bytes": 1811, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[34]/table-wrap[2]#db_ds_table-wrap2_reqid_", "version": null, "note": "GO annotation significantly related to target genes", "structure": {"pmcid": "PMC5759858", "section_index": 34, "section_title": "Supplementary Materials", "row_count": 18, "column_count": 4}, "table": {"label": "Table S2", "caption": "GO annotation significantly related to target genes", "rows": [["Term", "Count", "P-value", "Genes"], ["Lymphangiogenesis", "3", "0.0043", "PPP3CB, FLT4, BMPR2"], ["Transmembrane receptor protein serine/threonine kinase activity", "3", "0.0069", "LTBP4, LTBP1, BMPR2"], ["Feeding behavior", "7", "0.0078", "MCHR1, PPYR1, OPRD1, GLS, ASIP, PHF21A, IAPP"], ["RNA polymerase II carboxy-terminal domain kinase activity", "3", "0.0043", "GTF2H1, CDK9, GTF2H4"], ["Copper chaperone activity", "2", "0.0077", "PARK7, CCS"], ["Fatty acid elongation, saturated fatty acid", "2", "0.0077", "ELOVL4, ELOVL6"], ["Fatty acid elongation", "3", "0.0029", "ELOVL2, ELOVL4, ELOVL6"], ["Intracellular receptor signaling pathway", "13", "0.0090", "ZNF536, CCNE1, DCBLD2, PGR, MAP3K7, GPR56, ITCH, NOD1, KANK2, THRA, PARK7, RXRB, DDX5"], ["Negative regulation of protein complex assembly", "7", "0.0071", "THRA, HEY2, SPTAN1, MAP3K7, OPRD1, MAPRE1, PARK7"], ["Positive regulation of stress-activated MAPK cascade", "8", "0.0064", "IL1A, FLT4, MAP3K10, TNFSF11, NOD1, HIPK2, MAP3K7, STK25"], ["Lymph vessel morphogenesis", "3", "0.0059", "PPP3CB, FLT4, BMPR2"], ["Intrinsic apoptotic signaling pathway in response to hydrogen peroxide", "2", "0.0077", "PARK7, STK25"], ["Paracrine signaling", "2", "0.0077", "TNFSF11, PGR"], ["Sertoli cell development", "3", "0.0059", "DMRT1, ARID4B, SDC1"], ["Positive regulation of stress-activated protein kinase signaling cascade", "8", "0.0067", "IL1A, FLT4, MAP3K10, TNFSF11, NOD1, HIPK2, MAP3K7, STK25"], ["Serine/threonine protein kinase complex", "5", "0.0072", "GTF2H1, CDK9, MAP3K7, RB1CC1, GTF2H4"], ["Protein kinase complex", "7", "0.0026", "GTF2H1, CDK9, CCNE1, PRKAB2, GTF2H4, MAP3K7, RB1CC1"]], "row_count": 18, "column_count": 4, "numeric_cells": 40, "header_rows": 1, "locator": "section[34]/table-wrap[2]#db_ds_table-wrap2_reqid_"}}, {"id": "asset:table:pmid:29379305:9", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:aadde1c6a439c75f2573a96c3bacdd032673e288591d4c3a3b6076967aca998a", "bytes": 1308, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[34]/table-wrap[3]#db_ds_table-wrap3_reqid_", "version": null, "note": "The KEGG pathway significantly related to target genes", "structure": {"pmcid": "PMC5759858", "section_index": 34, "section_title": "Supplementary Materials", "row_count": 15, "column_count": 4}, "table": {"label": "Table S3", "caption": "The KEGG pathway significantly related to target genes", "rows": [["Term", "Count", "P-value", "Genes"], ["Arginine biosynthesis", "3", "0.0100", "ARG2, GOT2, GLS"], ["Fatty acid elongation", "3", "0.0171", "ELOVL2, ELOVL4, ELOVL6"], ["Nucleotide excision repair", "4", "0.0178", "GTF2H1, LIG1, RAD23B, GTF2H4"], ["Osteoclast differentiation", "7", "0.0195", "IL1A, CAMK4, TNFSF11, NCF4, PPP3CB, MAP3K7, SOCS3"], ["Rheumatoid arthritis", "5", "0.0379", "ITGAL, TNFSF11, IL8, MMP3, IL1A"], ["Phenylalanine metabolism", "2", "0.0128", "GLYAT, GOT2"], ["Selenocompound metabolism", "2", "0.0128", "SEPHS1, TXNRD1"], ["Fat digestion and absorption", "3", "0.0152", "PNLIPRP1, ABCA1, GOT2"], ["Ubiquitin-mediated proteolysis", "6", "0.0235", "PIAS3, CBL, TRIM32, ITCH, TRIM37, SOCS3"], ["Biosynthesis of amino acids", "4", "0.0276", "ARG2, GOT2, RPE, MAT2B"], ["Transcriptional misregulation in cancer", "7", "0.0351", "CDK9, MMP3, IL8, PAX5, RXRB, CCNA1, DDX5"], ["RNA degradation", "4", "0.0354", "DDX6, CNOT6, 10200, CNOT4"], ["Biosynthesis of unsaturated fatty acids", "2", "0.0459", "ELOVL2, ELOVL6"], ["Non-alcoholic fatty liver disease (NAFLD)", "6", "0.0500", "IL1A, PRKAB2, IL8, ITCH, NDUFA4L2, SOCS3"]], "row_count": 15, "column_count": 4, "numeric_cells": 33, "header_rows": 1, "locator": "section[34]/table-wrap[3]#db_ds_table-wrap3_reqid_"}}], "gaps": ["asset:data:geo:GSE39040 not downloaded", "asset:data:geo:GSE39040 licence not read", "asset:data:geo:GSE39052 not downloaded", "asset:data:geo:GSE39052 licence not read", "asset:data:geo:GSE79181 not downloaded", "asset:data:geo:GSE79181 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": "With expression values of the optimal feature combination of miRNAs as variables, associations of optimal feature miRNAs with recurrence time were studied by Cox regression analysis using the coxph R function of the survival package in R language."}}, {"id": "method-2", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "random forest"}}, {"id": "method-3", "family": "machine_learning", "specific": "support_vector_machine", "label": "Machine learning", "dsl_operations": ["train_classifier", "cross_validate", "roc_auc"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 0.7, "band": "medium", "quote": "support vector machine"}}], "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": ["GSE39040", "GSE39052", "GSE79181"], "resolved_accessions": ["GSE39040", "GSE39052", "GSE79181"], "statements": ["Three miRNA expression profiles, named GSE39040, GSE39052, and GSE79181, were achieved, among which the former two emerged from the platform “GPL15762 Illumina Human v2 MicroRNA Expression BeadChip”, whereas the last one arose from the platform “GPL15497 Applied Biosystems TaqMan Array Human MicroRNA Cards”. There were 23, 15, and 14 osteosarcoma recurrence samples, and 42, 11, and 9 osteosarcoma non-recurrence samples in these three datasets, separately."], "basis": "The paper names GSE39040, GSE39052, GSE79181 in GEO DataSets 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:29379305", "data:geo:GSE39040", "asset:table:pmid:29379305:1", "asset:table:pmid:29379305:2", "asset:table:pmid:29379305:3", "asset:table:pmid:29379305:4", "asset:table:pmid:29379305:5", "asset:table:pmid:29379305:6", "asset:table:pmid:29379305:7", "asset:table:pmid:29379305:8", "asset:table:pmid:29379305:9"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE39040"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:29Z", "independence": "same_provider"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 8, "usage": {"prompt_tokens": 140010, "completion_tokens": 6107, "cached_tokens": 2113}}, "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:29379305", "type": "paper", "label": "pmid:29379305"}, {"id": "source:pmid:29379305", "type": "manuscript", "label": "PMID 29379305 full text"}, {"id": "data:geo:GSE39040", "type": "dataset", "label": "GEO GSE39040"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29379305", "type": "paper", "label": "pmid:29379305"}, {"id": "source:pmid:29379305", "type": "manuscript", "label": "PMID 29379305 full text"}, {"id": "data:geo:GSE39040", "type": "dataset", "label": "GEO GSE39040"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29379305", "type": "extraction", "used": ["source:pmid:29379305"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE39040", "type": "accession_resolution", "used": ["data:geo:GSE39040"], "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:29379305", "parent_hash": "sha256:813dfbcaaf6cd7d4dfc7dfb0f2c347a05e7743a1f642a3256b68261652ff4512", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE39040 licence not read", "asset:data:geo:GSE39040 not downloaded", "asset:data:geo:GSE39052 licence not read", "asset:data:geo:GSE39052 not downloaded", "asset:data:geo:GSE79181 licence not read", "asset:data:geo:GSE79181 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": ["With expression values of the optimal feature combination of miRNAs as variables, associations of optimal feature miRNAs with recurrence time were studied by Cox regression analysis using the coxph R function of the survival package in R language."], "order_basis": "analysis_only", "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":"2026-11-04T02:46:42+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}}}