{"data":{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35116817", "kind": "science-record", "revision": 5, "content_hash": "sha256:063b2f6362f4aee3cb518b2455879272251a5a6595185e572da7d68f4b7b6912", "created_at": "2026-11-01T17:36:51Z", "updated_at": "2026-11-01T22:05:45Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of high expression profiles of miR-31-5p and its vital role in lung squamous cell carcinoma: a survey based on qRT-PCR and bioinformatics analysis.", "doi": "10.21037/tcr.2019.04.21", "pmid": "35116817", "authors": ["Xiao-Jv Chi", "Li-Li Wei", "Qing Bu", "Ning Mo", "Xin Yu Chen", "Dong Lan", "Qing Niao Zhou"], "journal": "Translational cancer research", "year": 2019, "abstract": "BACKGROUND: The function of miR-31-5p in lung squamous cell carcinoma (LUSC) remains unclear, therefore, a systematic study was performed for the clinical significance and molecular mechanism of miR-31-5p in LUSC.\nMETHODS: Quantitative real-time reverse transcription PCR (qRT-PCR) was utilized to test the expression level of miR-31-5p in 88 LUSC tissue samples and their matching normal tissues. Data from Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) were also utilized to confirm the expression level and clinical value of miR-31-5p in LUSC. The potential target genes of miR-31-5p were predicted by several online predicted software. Gene ontology (GO), protein-protein interaction (PPI) and pathway analysis were utilized to investigate the underlying molecular mechanism of miR-31-5p in LUSC.\nRESULTS: The result from qRT-PCR found that there was significant difference of miR-31-5p between LUSC and normal tissues (P<0.001). Meanwhile, Data from TCGA also showed a higher expression of miR-31-5p in LUSC tissues than that in the normal tissues (P<0.001). on the basis of the data of GEO database, five GEO datasets indicated that the expression of miR-31-5p in LUSC tissues was significantly higher than that in normal lung tissues, include GSE51858 (P=0.025), GSE74190 (P<0.000), GSE16025 (P=0.031), GSE25508 (P=0.0.01), and GSE47525 (P=0.049). Moreover, in consideration of the meta-analysis, 1,012 clinical specimens were systematically analyzed via meta-analysis, clinical specimens were systematically analyzed via meta-analysis, and the results showed that the expression of miR-31-5p in LUSC was significantly higher than in the adjacent lung tissues (SMD =0, CI: 1.08-1.45, Z=13.30, P=0.000). In addition, result from GO and pathway analyses showed that potential target genes of miR-31-5p were significantly associated with 20 GO terms and 5 pathways, such as signal transduction, transmembrane receptor protein tyrosine kinase activity, plasma membrane and Rap1 signaling pathway. Meanwhile, we also found thatmiR-31-5p target genes were related to the Rap1 signaling pathway, Oxytocin signaling pathway and Proteoglycans in cancer. Furthermore, six hub genes were identified from PPI and three hub genes, including ADCY6, ADCY9 and EGFR, proved to coexist in the Rap1 signaling pathway, oxytocin signaling pathway and Melanogenesis simultaneously.\nCONCLUSIONS: According to what has been discussed above, we speculated that miR-31-5p may play a vital role in the occurrence and development of LUSC.", "claims": [{"id": "claim-method", "statement": "StataSE 12.0 was used for the meta-analysis of the data and SMD <0 and 95% CI did not cross zero represented miR-31-5p had a lower expression in LUSC tissues than in normal specimens.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116817", "locator": "sections[9] \"Statistical analyses\" paragraph 2", "quote": "StataSE 12.0 was used for the meta-analysis of the data and SMD <0 and 95% CI did not cross zero represented miR-31-5p had a lower expression in LUSC tissues than in normal specimens."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35116817", "locator": "sections[5] \"Information extraction of miR-31-5p in LUSC from GEO and TCGA datasets\" paragraph 2", "quote": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC."}, {"asset": "source:pmid:35116817", "locator": "sections[11] \"High expression of miR-31-5p in LUSC\" paragraph 4", "quote": "Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Meanwhile, the meta-analysis result of all the data in the current study (PCR, TCGA, GEO included) showed that the expression of miR-31-5p significantly increased in patients with LUSC than the controls (SMD =0, 95% CI: 1.08–1.45, Z=13.30, P=0.000, Figure 7).", "kind": "quantitative", "target": {"value": 95.0, "unit": "per cent", "tolerance": null, "source": "Meanwhile, the meta-analysis result of all the data in the current study (PCR, TCGA, GEO included) showed that the expression of miR-31-5p significantly increased in patients with LUSC than the controls (SMD =0, 95% CI: 1.08–1.45, Z=13.30, P=0.000, Figure 7)."}, "evidence": [{"asset": "source:pmid:35116817", "locator": "sections[12] \"Meta-analysis of miR-31-5p expression in LUSC\" paragraph 5", "quote": "Meanwhile, the meta-analysis result of all the data in the current study (PCR, TCGA, GEO included) showed that the expression of miR-31-5p significantly increased in patients with LUSC than the controls (SMD =0, 95% CI: 1.08–1.45, Z=13.30, P=0.000, Figure 7)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Meanwhile, the meta-analysis result of all the data in the current study (PCR, TCGA, GEO included) showed that the expression of miR-31-5p significantly increased in patients with LUSC than the controls (SMD =0, 95% CI: 1.08–1.45, Z=13.30, P=0.000, Figure 7).", "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:35116817"], "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:GSE16025"], "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:GSE16025"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35116817", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr.2019.04.21", "sha256": "sha256:beaf3e2e1c3fa5216c05d5e5bcdce56649bac5491c6b594dfdb688306e4f9d92", "bytes": 27713, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr.2019.04.21", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8798478", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16025", "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=GSE16025", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16025", "version": null, "note": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM400970", "GSM400971", "GSM400972", "GSM400973", "GSM400974", "GSM400975", "GSM400976", "GSM400977", "GSM400978", "GSM400979", "GSM400980", "GSM400981", "GSM400982", "GSM400983", "GSM400984", "GSM400985", "GSM400986", "GSM400987", "GSM400988", "GSM400989", "GSM400990", "GSM400991", "GSM400992", "GSM400993", "GSM400994", "GSM400995", "GSM400996", "GSM400997", "GSM400998", "GSM400999", "GSM401000", "GSM401001", "GSM401002", "GSM401003", "GSM401004", "GSM401005", "GSM401006", "GSM401007", "GSM401008", "GSM401009", "GSM401010", "GSM401011", "GSM401012", "GSM401013", "GSM401014", "GSM401015", "GSM401016", "GSM401017", "GSM401018", "GSM401019", "GSM401020", "GSM401021", "GSM401022", "GSM401023", "GSM401024", "GSM401025", "GSM401026", "GSM401027", "GSM401028", "GSM401029", "GSM401030", "GSM401031", "GSM401032", "GSM401033", "GSM401034", "GSM401035", "GSM401036", "GSM401037", "GSM401038", "GSM401039", "GSM401040"], "sample_count": 71, "group_sizes": null, "group_sizes_basis": null, "platform": "5106", "taxon": "Mus musculus; Rattus norvegicus; Homo sapiens", "title": "miRNA prognostic profiles in lung cancer", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE25508", "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=GSE25508", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25508", "version": null, "note": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM627217", "GSM627218", "GSM627219", "GSM627220", "GSM627221", "GSM627222", "GSM627223", "GSM627224", "GSM627225", "GSM627226", "GSM627227", "GSM627228", "GSM627229", "GSM627230", "GSM627231", "GSM627232", "GSM627233", "GSM627234", "GSM627235", "GSM627236", "GSM627237", "GSM627238", "GSM627239", "GSM627240", "GSM627241", "GSM627242", "GSM627243", "GSM627244", "GSM627245", "GSM627246", "GSM627247", "GSM627248", "GSM627249", "GSM627250", "GSM630014", "GSM630015", "GSM630016", "GSM630017", "GSM630018", "GSM630019", "GSM630020", "GSM630021", "GSM630022", "GSM630023", "GSM630024", "GSM630025", "GSM630026", "GSM630027", "GSM630028", "GSM630029", "GSM630030", "GSM630031", "GSM630032", "GSM630033", "GSM630034", "GSM630035", "GSM630036", "GSM630037", "GSM630038", "GSM630039"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "7731", "taxon": "Homo sapiens", "title": "Integrative Analysis of microRNA, mRNA and DNA Copy Number Data Reveals Asbestos-Related Changes in Non-Small Cell Lung Cancer", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE40738", "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=GSE40738", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE40738", "version": null, "note": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1000223", "GSM1000224", "GSM1000225", "GSM1000226", "GSM1000227", "GSM1000228", "GSM1000229", "GSM1000230", "GSM1000231", "GSM1000232", "GSM1000233", "GSM1000234", "GSM1000235", "GSM1000236", "GSM1000237", "GSM1000238", "GSM1000239", "GSM1000240", "GSM1000241", "GSM1000242", "GSM1000243", "GSM1000244", "GSM1000245", "GSM1000246", "GSM1000247", "GSM1000248", "GSM1000249", "GSM1000250", "GSM1000251", "GSM1000252", "GSM1000253", "GSM1000254", "GSM1000255", "GSM1000256", "GSM1000257", "GSM1000258", "GSM1000259", "GSM1000260", "GSM1000261", "GSM1000262", "GSM1000263", "GSM1000264", "GSM1000265", "GSM1000266", "GSM1000267", "GSM1000268", "GSM1000269", "GSM1000270", "GSM1000271", "GSM1000272", "GSM1000273", "GSM1000274", "GSM1000275", "GSM1000276", "GSM1000277", "GSM1000278", "GSM1000279", "GSM1000280", "GSM1000281", "GSM1000282", "GSM1000283", "GSM1000284", "GSM1000285", "GSM1000286", "GSM1000287", "GSM1000288", "GSM1000289", "GSM1000290", "GSM1000291", "GSM1000292", "GSM1000293", "GSM1000294", "GSM1000295", "GSM1000296", "GSM1000297", "GSM1000298", "GSM1000299", "GSM1000300", "GSM1000301", "GSM1000302", "GSM1000303", "GSM1000304", "GSM1000305", "GSM1000306", "GSM1000307", "GSM1000308", "GSM1000309", "GSM1000310", "GSM1000311", "GSM1000312", "GSM1000313", "GSM1000314", "GSM1000315", "GSM1000316", "GSM1000317", "GSM1000318", "GSM1000319", "GSM1000320", "GSM1000321", "GSM1000322", "GSM1000323", "GSM1000324", "GSM1000325", "GSM1000326", "GSM1000327", "GSM1000328", "GSM1000329", "GSM1000330", "GSM1000331", "GSM1000332", "GSM1000333", "GSM1000334", "GSM1000335", "GSM1000336", "GSM1000337", "GSM1000338", "GSM1000339", "GSM1000340", "GSM1000341", "GSM1000342", "GSM1000343", "GSM1000344", "GSM1000345", "GSM1000346", "GSM1000347", "GSM1000348", "GSM1000349", "GSM1000350", "GSM1000351", "GSM1000352", "GSM1000353", "GSM1000354", "GSM1000355", "GSM1000356", "GSM1000357", "GSM1000358", "GSM1000359", "GSM1000360", "GSM1000361", "GSM1000362", "GSM1000363", "GSM1000364", "GSM1000365", "GSM1000366", "GSM1000367", "GSM1000368", "GSM1000369", "GSM1000370", "GSM1000371", "GSM1000372", "GSM1000373", "GSM1000374", "GSM1000375", "GSM1000376", "GSM1000377", "GSM1000378", "GSM1000379", "GSM1000380", "GSM1000381", "GSM1000382", "GSM1000383", "GSM1000384", "GSM1000385", "GSM1000386", "GSM1000387", "GSM1000388", "GSM1000389", "GSM1000390", "GSM1000391", "GSM1000392", "GSM1000393", "GSM1000394", "GSM1000395", "GSM1000396", "GSM1000397", "GSM1000398", "GSM1000399"], "sample_count": 177, "group_sizes": null, "group_sizes_basis": null, "platform": "16016", "taxon": "Human alphaherpesvirus 2; Cytomegalovirus; Lymphocryptovirus; Betapolyomavirus macacae; Murid gammaherpesvirus 4; Rattus norvegicus; JC polyomavirus; Betapolyomavirus hominis; Homo sapiens; Mus musculus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Rhadinovirus; Human immunodeficiency virus 1; Merkel cell polyomavirus", "title": "Whole blood microRNA expression in human lung cancer", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE47525", "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=GSE47525", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE47525", "version": null, "note": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1151548", "GSM1151549", "GSM1151550", "GSM1151551", "GSM1151552", "GSM1151553", "GSM1151554", "GSM1151555", "GSM1151556", "GSM1151557", "GSM1151558", "GSM1151559", "GSM1151560", "GSM1151561", "GSM1151562", "GSM1151563", "GSM1151564", "GSM1151565", "GSM1151566", "GSM1151567", "GSM1151568", "GSM1151569", "GSM1151570", "GSM1151571", "GSM1151572", "GSM1151573", "GSM1151574", "GSM1151575", "GSM1151576", "GSM1151577", "GSM1151578", "GSM1151579"], "sample_count": 32, "group_sizes": null, "group_sizes_basis": null, "platform": "17222", "taxon": "Homo sapiens", "title": "DNA damage responsive microRNAs misexpressed in human cancer regulate chemotherapy sensitivity (lung tumors)", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE51853", "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=GSE51853", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51853", "version": null, "note": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1253944", "GSM1253945", "GSM1253946", "GSM1253947", "GSM1253948", "GSM1253949", "GSM1253950", "GSM1253951", "GSM1253952", "GSM1253953", "GSM1253954", "GSM1253955", "GSM1253956", "GSM1253957", "GSM1253958", "GSM1253959", "GSM1253960", "GSM1253961", "GSM1253962", "GSM1253963", "GSM1253964", "GSM1253965", "GSM1253966", "GSM1253967", "GSM1253968", "GSM1253969", "GSM1253970", "GSM1253971", "GSM1253972", "GSM1253973", "GSM1253974", "GSM1253975", "GSM1253976", "GSM1253977", "GSM1253978", "GSM1253979", "GSM1253980", "GSM1253981", "GSM1253982", "GSM1253983", "GSM1253984", "GSM1253985", "GSM1253986", "GSM1253987", "GSM1253988", "GSM1253989", "GSM1253990", "GSM1253991", "GSM1253992", "GSM1253993", "GSM1253994", "GSM1253995", "GSM1253996", "GSM1253997", "GSM1253998", "GSM1253999", "GSM1254000", "GSM1254001", "GSM1254002", "GSM1254003", "GSM1254004", "GSM1254005", "GSM1254006", "GSM1254007", "GSM1254008", "GSM1254009", "GSM1254010", "GSM1254011", "GSM1254012", "GSM1254013", "GSM1254014", "GSM1254015", "GSM1254016", "GSM1254017", "GSM1254018", "GSM1254019", "GSM1254020", "GSM1254021", "GSM1254022", "GSM1254023", "GSM1254024", "GSM1254025", "GSM1254026", "GSM1254027", "GSM1254028", "GSM1254029", "GSM1254030", "GSM1254031", "GSM1254032", "GSM1254033", "GSM1254034", "GSM1254035", "GSM1254036", "GSM1254037", "GSM1254038", "GSM1254039", "GSM1254040", "GSM1254041", "GSM1254042", "GSM1254043", "GSM1254044", "GSM1254045", "GSM1254046", "GSM1254047", "GSM1254048", "GSM1254049", "GSM1254050", "GSM1254051", "GSM1254052", "GSM1254053", "GSM1254054", "GSM1254055", "GSM1254056", "GSM1254057", "GSM1254058", "GSM1254059", "GSM1254060", "GSM1254061", "GSM1254062", "GSM1254063", "GSM1254064", "GSM1254065", "GSM1254066", "GSM1254067", "GSM1254068", "GSM1254069", "GSM1254070", "GSM1254071", "GSM1254072", "GSM1254073", "GSM1254074"], "sample_count": 131, "group_sizes": null, "group_sizes_basis": null, "platform": "7341", "taxon": "Homo sapiens", "title": "Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features [miRNA analysis - miRNA Microarray, pre-commercial version 6.0]", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE74190", "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=GSE74190", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE74190", "version": null, "note": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1913414", "GSM1913415", "GSM1913416", "GSM1913417", "GSM1913418", "GSM1913419", "GSM1913420", "GSM1913421", "GSM1913422", "GSM1913423", "GSM1913424", "GSM1913425", "GSM1913426", "GSM1913427", "GSM1913428", "GSM1913429", "GSM1913430", "GSM1913431", "GSM1913432", "GSM1913433", "GSM1913434", "GSM1913435", "GSM1913436", "GSM1913437", "GSM1913438", "GSM1913439", "GSM1913440", "GSM1913441", "GSM1913442", "GSM1913443", "GSM1913444", "GSM1913445", "GSM1913446", "GSM1913447", "GSM1913448", "GSM1913449", "GSM1913450", "GSM1913451", "GSM1913452", "GSM1913453", "GSM1913454", "GSM1913455", "GSM1913456", "GSM1913457", "GSM1913458", "GSM1913459", "GSM1913460", "GSM1913461", "GSM1913462", "GSM1913463", "GSM1913464", "GSM1913465", "GSM1913466", "GSM1913467", "GSM1913468", "GSM1913469", "GSM1913470", "GSM1913471", "GSM1913472", "GSM1913473", "GSM1913474", "GSM1913475", "GSM1913476", "GSM1913477", "GSM1913478", "GSM1913479", "GSM1913480", "GSM1913481", "GSM1913482", "GSM1913483", "GSM1913484", "GSM1913485", "GSM1913486", "GSM1913487", "GSM1913488", "GSM1913489", "GSM1913490", "GSM1913491", "GSM1913492", "GSM1913493", "GSM1913494", "GSM1913495", "GSM1913496", "GSM1913497", "GSM1913498", "GSM1913499", "GSM1913500", "GSM1913501", "GSM1913502", "GSM1913503", "GSM1913504", "GSM1913505", "GSM1913506", "GSM1913507", "GSM1913508", "GSM1913509", "GSM1913510", "GSM1913511", "GSM1913512", "GSM1913513", "GSM1913514", "GSM1913515", "GSM1913516", "GSM1913517", "GSM1913518", "GSM1913519", "GSM1913520", "GSM1913521", "GSM1913522", "GSM1913523", "GSM1913524", "GSM1913525", "GSM1913526", "GSM1913527", "GSM1913528", "GSM1913529", "GSM1913530", "GSM1913531", "GSM1913532", "GSM1913533", "GSM1913534", "GSM1913535", "GSM1913536", "GSM1913537", "GSM1913538", "GSM1913539", "GSM1913540", "GSM1913541", "GSM1913542", "GSM1913543", "GSM1913544", "GSM1913545", "GSM1913546", "GSM1913547", "GSM1913548", "GSM1913549"], "sample_count": 136, "group_sizes": null, "group_sizes_basis": null, "platform": "19622", "taxon": "Homo sapiens", "title": "The miRNA expression profiles in three subtypes of lung carcinomas", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE16025 not downloaded", "asset:data:geo:GSE16025 licence not read", "asset:data:geo:GSE25508 not downloaded", "asset:data:geo:GSE25508 licence not read", "asset:data:geo:GSE40738 not downloaded", "asset:data:geo:GSE40738 licence not read", "asset:data:geo:GSE47525 not downloaded", "asset:data:geo:GSE47525 licence not read", "asset:data:geo:GSE51853 not downloaded", "asset:data:geo:GSE51853 licence not read", "asset:data:geo:GSE74190 not downloaded", "asset:data:geo:GSE74190 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-2", "family": null, "specific": null, "label": "Meta-analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "StataSE 12.0 was used for the meta-analysis of the data and SMD <0 and 95% CI did not cross zero represented miR-31-5p had a lower expression in LUSC tissues than in normal specimens."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 95.0, "unit": "per cent", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}, {"id": "target-published-estimate-p-value", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.0, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE16025", "GSE25508", "GSE47525", "GSE51853", "GSE74190", "GSE40738"], "resolved_accessions": ["GSE16025", "GSE25508", "GSE47525", "GSE51853", "GSE74190", "GSE40738"], "statements": ["The Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/) (26) was used for extracting the expression information of miR-31-5p in LUSC. Respect to the GEO database, five databases (GSE16025, GSE25508, GSE47525, GSE51853, GSE74190) supported the viewpoint that the up-regulated expression of miR-31-5p in LUSC patients compared to the corresponding controls (P<0.05) (Figure 3)."], "basis": "The paper names GSE16025, GSE25508, GSE47525, GSE51853, GSE74190, GSE40738 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:35116817", "data:geo:GSE16025"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE16025"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:32:28Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 8876, "completion_tokens": 3277, "cached_tokens": 264}}, "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:35116817", "type": "paper", "label": "pmid:35116817"}, {"id": "source:pmid:35116817", "type": "manuscript", "label": "PMID 35116817 full text"}, {"id": "data:geo:GSE16025", "type": "dataset", "label": "GEO GSE16025"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35116817", "type": "paper", "label": "pmid:35116817"}, {"id": "source:pmid:35116817", "type": "manuscript", "label": "PMID 35116817 full text"}, {"id": "data:geo:GSE16025", "type": "dataset", "label": "GEO GSE16025"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35116817", "type": "extraction", "used": ["source:pmid:35116817"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE16025", "type": "accession_resolution", "used": ["data:geo:GSE16025"], "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:35116817", "parent_hash": "sha256:7ab8e2f7a3c56ae940703be843ed2d329a00e4fc78fc07a6c3c057794977a606", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE16025 licence not read", "asset:data:geo:GSE16025 not downloaded", "asset:data:geo:GSE25508 licence not read", "asset:data:geo:GSE25508 not downloaded", "asset:data:geo:GSE40738 licence not read", "asset:data:geo:GSE40738 not downloaded", "asset:data:geo:GSE47525 licence not read", "asset:data:geo:GSE47525 not downloaded", "asset:data:geo:GSE51853 licence not read", "asset:data:geo:GSE51853 not downloaded", "asset:data:geo:GSE74190 licence not read", "asset:data:geo:GSE74190 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "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":"2026-11-04T03:48:55+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}}}