Exploring the long noncoding RNAs-based biomarkers and pathogenesis of malignant transformation from dysplasia to oral squamous cell carcinoma by bioinformatics method.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31343435", "kind": "science-record", "revision": 5, "content_hash": "sha256:97fe88a30fc07c2288fe57caa3e24cb35ea857373cb7b39a4feb3fa5585b467c", "created_at": "2026-11-01T15:40:47Z", "updated_at": "2026-11-01T21:22:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the long noncoding RNAs-based biomarkers and pathogenesis of malignant transformation from dysplasia to oral squamous cell carcinoma by bioinformatics method.", "doi": "10.1097/CEJ.0000000000000527", "pmid": "31343435", "authors": ["Hongcheng Jia", "Xuan Wang", "Zheng Sun"], "journal": "European journal of cancer prevention : the official journal of the European Cancer Prevention Organisation (ECP)", "year": 2020, "abstract": "Long noncoding RNAs (lncRNAs) play an important role in many biological processes and carcinogenesis. We aimed to explore lncRNA-based pathogenesis, diagnostic biomarkers, and predictive factors of malignant transformation from dysplasia to oral squamous cell carcinoma (OSCC). Microarray data of GSE30784 consisting of 167 OSCC, 17 dysplasia, and 45 normal oral tissues were downloaded from the GEO database. The differentially expressed genes (DEGs) and lncRNAs between the three samples were identified using R, followed by lncRNA-mRNA coexpression and coregulation network analysis for the prediction of lncRNA target genes. Gene Ontology and Kyoto encydopedia of gene and genomes pathway analysis were performed to further characterize potential interactions. A total of 4462 DEGs and 76 differentially expressed lncRNAs were screened between the three groups, and 200 DEGs and only double homeobox A pseudogene 10 (DUXAP10) were screened among the three groups. A total of 1662 interactions of 46 lncRNAs and their coexpressed target genes were predicted, and 38 pairs of lncRNA-lncRNA coregulated 843 target genes. The coregulated target genes significantly enriched in antigen adaptive immune response, activation of phagocytosis receptor signaling, mast granule NF-κB inflammation, etc. Overall, lncRNAs were differentially expressed in OSCC and dysplasia. The target genes might play an important role in the carcinogenesis and development of OSCC. These results improve our understanding regarding the lncRNA-based pathogenesis and identify some potential targets for early diagnosis of malignant transformation from dysplasia to OSCC.", "claims": [{"id": "claim-method", "statement": "Functional enrichment analysis of coregulated genes was done by Maere et al. (2005). Functional enrichment analysis of coexpressed genes was done by Huang et al. (2009).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31343435", "locator": "sections[7] \"Functional analysis of target genes regulated by long noncoding RNAs\" paragraph 2", "quote": "Functional enrichment analysis of coregulated genes was done by Maere et al. (2005). Functional enrichment analysis of coexpressed genes was done by Huang et al. (2009)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data (GSE30784) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The gene chip data were completed and submitted to GEO by Chen et al. (2008) from the Fred Hutchinson Cancer Research Center, which included 167 cases of OSCC, 17 cases of atypical hyperplasia, and 45 cases of normal control. The platform is GPL570, namely, the Affymetrix U133 2 Plus GeneChip arrays. GEOquery package in R language was used to obtain the gene chip expression data whose accession number is GSE30784, and its acquisition address is https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30784/matrix/GSE30784_series_matrix.txt.gz. The dataset contains 229 samples and expression information of 54 675 probes. At the same time, the annotation information of the probes, such as the associated gene symbols, Entrez Gene ID and gene name, and the clinical annotation information of the sample, such as age, gender, and disease status (cancer, dysplasia and control), were also obtained.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31343435", "locator": "sections[3] \"Affymetrix microarray data\" paragraph 2", "quote": "The data (GSE30784) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/)."}, {"asset": "source:pmid:31343435", "locator": "sections[3] \"Affymetrix microarray data\" paragraph 2", "quote": "The gene chip data were completed and submitted to GEO by Chen et al."}, {"asset": "source:pmid:31343435", "locator": "sections[3] \"Affymetrix microarray data\" paragraph 2", "quote": "(2008) from the Fred Hutchinson Cancer Research Center, which included 167 cases of OSCC, 17 cases of atypical hyperplasia, and 45 cases of normal control."}, {"asset": "source:pmid:31343435", "locator": "sections[3] \"Affymetrix microarray data\" paragraph 2", "quote": "The platform is GPL570, namely, the Affymetrix U133 2 Plus GeneChip arrays."}, {"asset": "source:pmid:31343435", "locator": "sections[4] \"Data preprocessing\" paragraph 2", "quote": "GEOquery package in R language was used to obtain the gene chip expression data whose accession number is GSE30784, and its acquisition address is https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30784/matrix/GSE30784_series_matrix.txt.gz."}, {"asset": "source:pmid:31343435", "locator": "sections[4] \"Data preprocessing\" paragraph 2", "quote": "The dataset contains 229 samples and expression information of 54 675 probes."}, {"asset": "source:pmid:31343435", "locator": "sections[4] \"Data preprocessing\" paragraph 2", "quote": "At the same time, the annotation information of the probes, such as the associated gene symbols, Entrez Gene ID and gene name, and the clinical annotation information of the sample, such as age, gender, and disease status (cancer, dysplasia and control), were also obtained."}], "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:31343435"], "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:GSE30784"], "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:GSE30784"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31343435", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1097/CEJ.0000000000000527", "sha256": "sha256:588ecb6b2df1bd8fb265b590cff214b9da3c09b8b6e4650e30152972009e0780", "bytes": 21900, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1097/CEJ.0000000000000527", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7012364", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE30784", "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=GSE30784", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE30784", "version": null, "note": "The data (GSE30784) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The gene chip data were completed and submitted to GEO by Chen et al. (2008) from the Fred Hutchinson Cancer Research Center, which included 167 cases of OSCC, 17 cases of atypical hyperplasia, and 45 cases of normal control. The platform is GPL570, namely, the Affymetrix U133 2 Plus GeneChip arrays. GEOquery package in R language was used to obtain the gene chip expression data whose accession number is GSE30784, and its acquisition address is https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30784/matrix/GSE30784_series_matrix.txt.gz. The dataset contains 229 samples and expression information of 54 675 probes. At the same time, the annotation information of the probes, such as the associated gene symbols, Entrez Gene ID and gene name, and the clinical annotation information of the sample, such as age, gender, and disease status (cancer, dysplasia and control), were also obtained.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data (GSE30784) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The gene chip data were completed and submitted to GEO by Chen et al. (2008) from the Fred Hutchinson Cancer Research Center, which included 167 cases of OSCC, 17 cases of atypical hyperplasia, and 45 cases of normal control. The platform is GPL570, namely, the Affymetrix U133 2 Plus GeneChip arrays. GEOquery package in R language was used to obtain the gene chip expression data whose accession number is GSE30784, and its acquisition address is https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30784/matrix/GSE30784_series_matrix.txt.gz. The dataset contains 229 samples and expression information of 54 675 probes. At the same time, the annotation information of the probes, such as the associated gene symbols, Entrez Gene ID and gene name, and the clinical annotation information of the sample, such as age, gender, and disease status (cancer, dysplasia and control), were also obtained.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM764749", "GSM764750", "GSM764751", "GSM764752", "GSM764753", "GSM764754", "GSM764755", "GSM764756", "GSM764757", "GSM764758", "GSM764759", "GSM764760", "GSM764761", "GSM764762", "GSM764763", "GSM764764", "GSM764765", "GSM764766", "GSM764767", "GSM764768", "GSM764769", "GSM764770", "GSM764771", "GSM764772", "GSM764773", "GSM764774", "GSM764775", "GSM764776", "GSM764777", "GSM764778", "GSM764779", "GSM764780", "GSM764781", "GSM764782", "GSM764783", "GSM764784", "GSM764785", "GSM764786", "GSM764787", "GSM764788", "GSM764789", "GSM764790", "GSM764791", "GSM764792", "GSM764793", "GSM764794", "GSM764795", "GSM764796", "GSM764797", "GSM764798", "GSM764799", "GSM764800", "GSM764801", "GSM764802", "GSM764803", "GSM764804", "GSM764805", "GSM764806", "GSM764807", "GSM764808", "GSM764809", "GSM764810", "GSM764811", "GSM764812", "GSM764813", "GSM764814", "GSM764815", "GSM764816", "GSM764817", "GSM764818", "GSM764819", "GSM764820", "GSM764821", "GSM764822", "GSM764823", "GSM764824", "GSM764825", "GSM764826", "GSM764827", "GSM764828", "GSM764829", "GSM764830", "GSM764831", "GSM764832", "GSM764833", "GSM764834", "GSM764835", "GSM764836", "GSM764837", "GSM764838", "GSM764839", "GSM764840", "GSM764841", "GSM764842", "GSM764843", "GSM764844", "GSM764845", "GSM764846", "GSM764847", "GSM764848", "GSM764849", "GSM764850", "GSM764851", "GSM764852", "GSM764853", "GSM764854", "GSM764855", "GSM764856", "GSM764857", "GSM764858", "GSM764859", "GSM764860", "GSM764861", "GSM764862", "GSM764863", "GSM764864", "GSM764865", "GSM764866", "GSM764867", "GSM764868", "GSM764869", "GSM764870", "GSM764871", "GSM764872", "GSM764873", "GSM764874", "GSM764875", "GSM764876", "GSM764877", "GSM764878", "GSM764879", "GSM764880", "GSM764881", "GSM764882", "GSM764883", "GSM764884", "GSM764885", "GSM764886", "GSM764887", "GSM764888", "GSM764889", "GSM764890", "GSM764891", "GSM764892", "GSM764893", "GSM764894", "GSM764895", "GSM764896", "GSM764897", "GSM764898", "GSM764899", "GSM764900", "GSM764901", "GSM764902", "GSM764903", "GSM764904", "GSM764905", "GSM764906", "GSM764907", "GSM764908", "GSM764909", "GSM764910", "GSM764911", "GSM764912", "GSM764913", "GSM764914", "GSM764915", "GSM764916", "GSM764917", "GSM764918", "GSM764919", "GSM764920", "GSM764921", "GSM764922", "GSM764923", "GSM764924", "GSM764925", "GSM764926", "GSM764927", "GSM764928", "GSM764929", "GSM764930", "GSM764931", "GSM764932", "GSM764933", "GSM764934", "GSM764935", "GSM764936", "GSM764937", "GSM764938", "GSM764939", "GSM764940", "GSM764941", "GSM764942", "GSM764943", "GSM764944", "GSM764945", "GSM764946", "GSM764947", "GSM764948", "GSM764949", "GSM764950", "GSM764951", "GSM764952", "GSM764953", "GSM764954", "GSM764955", "GSM764956", "GSM764957", "GSM764958", "GSM764959", "GSM764960", "GSM764961", "GSM764962", "GSM764963", "GSM764964", "GSM764965", "GSM764966", "GSM764967", "GSM764968", "GSM764969", "GSM764970", "GSM764971", "GSM764972", "GSM764973", "GSM764974", "GSM764975", "GSM764976", "GSM764977"], "sample_count": 229, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profiling of oral squamous cell carcinoma (OSCC)", "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:31343435:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:4de6ea95a4809a4b3bd23352e0ebd59a2b917d77ae98b55a21684fc4f40d83e4", "bytes": 256, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T1", "version": null, "note": "List of coexpressed long noncoding RNAs and the top 10 target genes in the group of dysplasia versus control", "structure": {"pmcid": "PMC7012364", "section_index": 10, "section_title": "Target genes of long noncoding RNAs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 1", "caption": "List of coexpressed long noncoding RNAs and the top 10 target genes in the group of dysplasia versus control", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:31343435:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:db1458200c20a890285cf572a33641442ebde99be359a393b4332b89030dcb1d", "bytes": 249, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[2]#T2", "version": null, "note": "List of coregulated long noncoding RNAs and the target genes in the group of dysplasia versus control", "structure": {"pmcid": "PMC7012364", "section_index": 10, "section_title": "Target genes of long noncoding RNAs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 2", "caption": "List of coregulated long noncoding RNAs and the target genes in the group of dysplasia versus control", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[2]#T2"}}, {"id": "asset:table:pmid:31343435:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:871e4d997dbea25221edad71025df165ea6c10754ae5b662f037c0e296eafe1d", "bytes": 253, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[3]#T3", "version": null, "note": "List of coexpressed long noncoding RNAs and the top 10 target genes in the group of cancer versus control", "structure": {"pmcid": "PMC7012364", "section_index": 10, "section_title": "Target genes of long noncoding RNAs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 3", "caption": "List of coexpressed long noncoding RNAs and the top 10 target genes in the group of cancer versus control", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[3]#T3"}}, {"id": "asset:table:pmid:31343435:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:798fd91e756065a0a7d3715ed653bf8cbe414ab12ffff67c78e2f371feadf3d8", "bytes": 253, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[4]#T4", "version": null, "note": "List of coregulated long noncoding RNAs and the top 10 target genes in the group of cancer versus control", "structure": {"pmcid": "PMC7012364", "section_index": 10, "section_title": "Target genes of long noncoding RNAs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 4", "caption": "List of coregulated long noncoding RNAs and the top 10 target genes in the group of cancer versus control", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[4]#T4"}}, {"id": "asset:table:pmid:31343435:5", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:66c372ff09dc1c6810a7aeac8ae34dfd3d0db44fd91a79c65bccf643980e75e2", "bytes": 248, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[5]#T5", "version": null, "note": "List of coexpressed long noncoding RNAs and the target genes in the group of cancer versus dysplasia", "structure": {"pmcid": "PMC7012364", "section_index": 10, "section_title": "Target genes of long noncoding RNAs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 5", "caption": "List of coexpressed long noncoding RNAs and the target genes in the group of cancer versus dysplasia", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[5]#T5"}}, {"id": "asset:table:pmid:31343435:6", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:64423e485f7f18c406e9330d9dfc8fee0a4bcce89af0f724c3c5160f44ba2ff5", "bytes": 248, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[6]#T6", "version": null, "note": "List of coregulated long noncoding RNAs and the target genes in the group of cancer versus dysplasia", "structure": {"pmcid": "PMC7012364", "section_index": 10, "section_title": "Target genes of long noncoding RNAs", "row_count": 0, "column_count": 0}, "table": {"label": "Table 6", "caption": "List of coregulated long noncoding RNAs and the target genes in the group of cancer versus dysplasia", "rows": [], "row_count": 0, "column_count": 0, "numeric_cells": 0, "header_rows": 0, "locator": "section[10]/table-wrap[6]#T6"}}], "gaps": ["asset:data:geo:GSE30784 not downloaded", "asset:data:geo:GSE30784 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Functional enrichment analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Functional enrichment analysis of coregulated genes was done by Maere et al. (2005). Functional enrichment analysis of coexpressed genes was done by Huang et al. (2009)."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Functional enrichment analysis), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE30784"], "resolved_accessions": ["GSE30784"], "statements": ["The data (GSE30784) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The gene chip data were completed and submitted to GEO by Chen et al. (2008) from the Fred Hutchinson Cancer Research Center, which included 167 cases of OSCC, 17 cases of atypical hyperplasia, and 45 cases of normal control. The platform is GPL570, namely, the Affymetrix U133 2 Plus GeneChip arrays. GEOquery package in R language was used to obtain the gene chip expression data whose accession number is GSE30784, and its acquisition address is https://ftp.ncbi.nlm.nih.gov/geo/series/GSE30nnn/GSE30784/matrix/GSE30784_series_matrix.txt.gz. The dataset contains 229 samples and expression information of 54 675 probes. At the same time, the annotation information of the probes, such as the associated gene symbols, Entrez Gene ID and gene name, and the clinical annotation information of the sample, such as age, gender, and disease status (cancer, dysplasia and control), were also obtained."], "basis": "The paper names GSE30784 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:31343435", "data:geo:GSE30784", "asset:table:pmid:31343435:1", "asset:table:pmid:31343435:2", "asset:table:pmid:31343435:3", "asset:table:pmid:31343435:4", "asset:table:pmid:31343435:5", "asset:table:pmid:31343435:6"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE30784"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:15:42Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 16167, "completion_tokens": 1551, "cached_tokens": 776}}, "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:31343435", "type": "paper", "label": "pmid:31343435"}, {"id": "source:pmid:31343435", "type": "manuscript", "label": "PMID 31343435 full text"}, {"id": "data:geo:GSE30784", "type": "dataset", "label": "GEO GSE30784"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31343435", "type": "paper", "label": "pmid:31343435"}, {"id": "source:pmid:31343435", "type": "manuscript", "label": "PMID 31343435 full text"}, {"id": "data:geo:GSE30784", "type": "dataset", "label": "GEO GSE30784"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31343435", "type": "extraction", "used": ["source:pmid:31343435"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE30784", "type": "accession_resolution", "used": ["data:geo:GSE30784"], "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:31343435", "parent_hash": "sha256:f348fa36cb8c67c7aeb191075f5c377c6484003596b6640449f129eb462f276e", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE30784 licence not read", "asset:data:geo:GSE30784 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["asia to oral squamous cell carcinoma (OSCC). Microarray data of GSE30784 consisting of 167 OSCC, 17"], "order_basis": "paper_text_order:402", "id": "assay:1"}]}