Database: The Journal of Biological Databases and Curation最新文献_第5页

TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes. TcEVdb：来自单细胞转录组的t细胞衍生的小细胞外囊泡数据库。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-28 DOI: 10.1093/database/baaf012

Tao Luo, Wen-Kang Shen, Chu-Yu Zhang, Dan-Dan Song, Xiu-Qing Zhang, An-Yuan Guo, Qian Lei

{"title":"TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes.","authors":"Tao Luo, Wen-Kang Shen, Chu-Yu Zhang, Dan-Dan Song, Xiu-Qing Zhang, An-Yuan Guo, Qian Lei","doi":"10.1093/database/baaf012","DOIUrl":"10.1093/database/baaf012","url":null,"abstract":"T-Cell-derived extracellular vesicles (TcEVs) play key roles in immune regulation and tumor microenvironment modulation. However, the heterogeneity of TcEV remains poorly understood due to technical limitations of EV analysis and the lack of comprehensive data. To address this, we constructed TcEVdb, a comprehensive database that explores the expression and cluster of TcEV by the SEVtras method from T-cell single-cell RNA sequencing data. TcEVdb contains 277 265 EV droplets from 51 T-cell types across 221 samples from 21 projects, covering 9 tissue sources and 23 disease conditions. The database provides two main functional modules. The Browse module enables users to investigate EV secretion activity indices across samples, visualize TcEV clusters, analyze differentially expressed genes (DEGs) and pathway enrichment in TcEV subpopulations, and compare TcEV transcriptomes with their cellular origins. The Search module allows users to query specific genes across all datasets and visualize their expression distribution. Furthermore, our analysis of TcEV in diffuse large B-cell lymphoma revealed increased EV secretion in CD4+ T exhausted cells compared to healthy controls. Subsequent analyses identified distinct droplet clusters with differential expression genes, including clusters enriched for genes associated with cell motility and mitochondrial function. Overall, TcEVdb serves as a comprehensive resource for exploring the transcriptome of TcEV, which will contribute to advancements in EV-based diagnostics and therapeutics across a wide range of diseases. Database URL: https://guolab.wchscu.cn/TcEVdb.","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11885782/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes. TcEVdb：来自单细胞转录组的t细胞衍生的小细胞外囊泡数据库。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-28 DOI: 10.1093/database/baaf012

Tao Luo, Wen-Kang Shen, Chu-Yu Zhang, Dan-Dan Song, Xiu-Qing Zhang, An-Yuan Guo, Qian Lei

{"title":"TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes.","authors":"Tao Luo, Wen-Kang Shen, Chu-Yu Zhang, Dan-Dan Song, Xiu-Qing Zhang, An-Yuan Guo, Qian Lei","doi":"10.1093/database/baaf012","DOIUrl":"https://doi.org/10.1093/database/baaf012","url":null,"abstract":"T-Cell-derived extracellular vesicles (TcEVs) play key roles in immune regulation and tumor microenvironment modulation. However, the heterogeneity of TcEV remains poorly understood due to technical limitations of EV analysis and the lack of comprehensive data. To address this, we constructed TcEVdb, a comprehensive database that explores the expression and cluster of TcEV by the SEVtras method from T-cell single-cell RNA sequencing data. TcEVdb contains 277 265 EV droplets from 51 T-cell types across 221 samples from 21 projects, covering 9 tissue sources and 23 disease conditions. The database provides two main functional modules. The Browse module enables users to investigate EV secretion activity indices across samples, visualize TcEV clusters, analyze differentially expressed genes (DEGs) and pathway enrichment in TcEV subpopulations, and compare TcEV transcriptomes with their cellular origins. The Search module allows users to query specific genes across all datasets and visualize their expression distribution. Furthermore, our analysis of TcEV in diffuse large B-cell lymphoma revealed increased EV secretion in CD4+ T exhausted cells compared to healthy controls. Subsequent analyses identified distinct droplet clusters with differential expression genes, including clusters enriched for genes associated with cell motility and mitochondrial function. Overall, TcEVdb serves as a comprehensive resource for exploring the transcriptome of TcEV, which will contribute to advancements in EV-based diagnostics and therapeutics across a wide range of diseases. Database URL: https://guolab.wchscu.cn/TcEVdb.","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126920","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MANUDB: database and application to retrieve and visualize mammalian NUMTs. 检索和可视化哺乳动物numt的数据库和应用程序。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-22 DOI: 10.1093/database/baaf009

Bálint Biró, Zoltán Gál, Zsófia Nagy, Juan Francisco Garcia, Tsend-Ayush Batbold, Orsolya Ivett Hoffmann

引用次数: 0

PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress. PotatoBSLnc：马铃薯长链非编码rna的资源库，以应对生物胁迫。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-22 DOI: 10.1093/database/baaf015

Pingping Huang, Weilin Cao, Zhaojun Li, Qingshuai Chen, Guangchao Wang, Bailing Zhou, Jihua Wang

{"title":"PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress.","authors":"Pingping Huang, Weilin Cao, Zhaojun Li, Qingshuai Chen, Guangchao Wang, Bailing Zhou, Jihua Wang","doi":"10.1093/database/baaf015","DOIUrl":"10.1093/database/baaf015","url":null,"abstract":"The biotic stress significantly influences the production of potato (Solanum tuberosum L.) all over the world. Long noncoding RNAs (lncRNAs) play key roles in the plant response to environmental stressors. However, their roles in potato resistance to pathogens, insects, and other biotic stress are still unclear. The PotatoBSLnc is a database for the study of potato lncRNAs in response to major biotic stress. Here, we collected 364 RNA sequencing (RNA-seq) data derived from 12 kinds of biotic stresses in 26 cultivars and wild potatoes. PotatoBSLnc currently contains 18 636 lncRNAs and 44 263 mRNAs. In addition, to select the functional lncRNAs and mRNAs under different stresses, the differential expression analyses and the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses related to the cis/trans-targets of differentially expressed lncRNAs (DElncRNAs) and to the differentially expressed mRNAs (DEmRNAs) were also conducted. The database contains five modules: Home, Browse, Expression, Biotic stress, and Download. Among these, the \"Browse\" module can be used to search detailed information about RNA-seq data (disease, cultivator, organ types, treatment of samples, and others), the exon numbers, length, location, and sequence of each lncRNA/mRNA. The \"Expression\" module can be used to search the transcripts per million/raw count value of lncRNAs/mRNAs at different RNA-seq data. The \"Biotic stress\" module shows the results of differential expression analyses under each of the 12 biotic stresses, the cis/trans-targets of DElncRNAs, the GO and KEGG analysis results of DEmRNAs, and the targets of DElncRNAs. The PotatoBSLnc platform provides researchers with detailed information on potato lncRNAs and mRNAs under biotic stress, which can speed up the breeding of resistant varieties based on the molecular methods. Database URL: https://www.sdklab-biophysics-dzu.net/PotatoBSLnc.","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11846501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143476331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MANUDB: database and application to retrieve and visualize mammalian NUMTs. 检索和可视化哺乳动物numt的数据库和应用程序。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-22 DOI: 10.1093/database/baaf009

Bálint Biró, Zoltán Gál, Zsófia Nagy, Juan Francisco Garcia, Tsend-Ayush Batbold, Orsolya Ivett Hoffmann

引用次数: 0

PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress. PotatoBSLnc：马铃薯长链非编码rna的资源库，以应对生物胁迫。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-22 DOI: 10.1093/database/baaf015

Pingping Huang, Weilin Cao, Zhaojun Li, Qingshuai Chen, Guangchao Wang, Bailing Zhou, Jihua Wang

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引用次数: 0

Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database. 将来自PubTator的人工智能文本挖掘集成到比较毒物基因组学数据库的手动管理工作流程中。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-21 DOI: 10.1093/database/baaf013

Thomas C Wiegers, Allan Peter Davis, Jolene Wiegers, Daniela Sciaky, Fern Barkalow, Brent Wyatt, Melissa Strong, Roy McMorran, Sakib Abrar, Carolyn J Mattingly

{"title":"Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database.","authors":"Thomas C Wiegers, Allan Peter Davis, Jolene Wiegers, Daniela Sciaky, Fern Barkalow, Brent Wyatt, Melissa Strong, Roy McMorran, Sakib Abrar, Carolyn J Mattingly","doi":"10.1093/database/baaf013","DOIUrl":"10.1093/database/baaf013","url":null,"abstract":"The Comparative Toxicogenomics Database (CTD) is a manually curated knowledge- and discovery-base that seeks to advance understanding about the relationship between environmental exposures and human health. CTD's manual curation process extracts from the biomedical literature molecular relationships between chemicals/drugs, genes/proteins, phenotypes, diseases, anatomical terms, and species. These relationships are organized in a highly systematic way in order to make them not only informative but also scientifically computational, enabling inferential hypotheses to be formed to address gaps in understanding. Integral to CTD's functionality is the use of structured, hierarchical ontologies and controlled vocabularies to describe these molecular relationships. Normalizing text (i.e. translating raw text from the literature into these controlled vocabularies) can be a time-consuming process for biocurators. To facilitate the normalization process and improve the efficiency with which our scientists curate the literature, CTD evaluated and integrated into the curation process PubTator 3.0, a state-of-the-art, AI-powered resource which extracts and normalizes from the literature many of the key biomedical concepts CTD curates. Here, we describe CTD's long-standing history with Natural Language Processing (NLP), how this history helped form our objectives for NLP integration, the evaluation of PubTator against our objectives, and the integration of PubTator into CTD's curation workflow. Database URL: https://ctdbase.org.","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11844237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143472396","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database. 将来自PubTator的人工智能文本挖掘集成到比较毒物基因组学数据库的手动管理工作流程中。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-21 DOI: 10.1093/database/baaf013

Thomas C Wiegers, Allan Peter Davis, Jolene Wiegers, Daniela Sciaky, Fern Barkalow, Brent Wyatt, Melissa Strong, Roy McMorran, Sakib Abrar, Carolyn J Mattingly

{"title":"Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database.","authors":"Thomas C Wiegers, Allan Peter Davis, Jolene Wiegers, Daniela Sciaky, Fern Barkalow, Brent Wyatt, Melissa Strong, Roy McMorran, Sakib Abrar, Carolyn J Mattingly","doi":"10.1093/database/baaf013","DOIUrl":"https://doi.org/10.1093/database/baaf013","url":null,"abstract":"The Comparative Toxicogenomics Database (CTD) is a manually curated knowledge- and discovery-base that seeks to advance understanding about the relationship between environmental exposures and human health. CTD's manual curation process extracts from the biomedical literature molecular relationships between chemicals/drugs, genes/proteins, phenotypes, diseases, anatomical terms, and species. These relationships are organized in a highly systematic way in order to make them not only informative but also scientifically computational, enabling inferential hypotheses to be formed to address gaps in understanding. Integral to CTD's functionality is the use of structured, hierarchical ontologies and controlled vocabularies to describe these molecular relationships. Normalizing text (i.e. translating raw text from the literature into these controlled vocabularies) can be a time-consuming process for biocurators. To facilitate the normalization process and improve the efficiency with which our scientists curate the literature, CTD evaluated and integrated into the curation process PubTator 3.0, a state-of-the-art, AI-powered resource which extracts and normalizes from the literature many of the key biomedical concepts CTD curates. Here, we describe CTD's long-standing history with Natural Language Processing (NLP), how this history helped form our objectives for NLP integration, the evaluation of PubTator against our objectives, and the integration of PubTator into CTD's curation workflow. Database URL: https://ctdbase.org.","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126865","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design. LICEDB：用于工业应用和AI酶设计的轻工业核心酶数据库。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-19 DOI: 10.1093/database/baaf001

Lei Gong, Fufeng Liu, Chuanxi Zhang, Yongfan Ming, Yulan Mou, ZhaoTing Yuan, Haiming Jiang, Bei Gao, Fuping Lu, Lujia Zhang

{"title":"LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design.","authors":"Lei Gong, Fufeng Liu, Chuanxi Zhang, Yongfan Ming, Yulan Mou, ZhaoTing Yuan, Haiming Jiang, Bei Gao, Fuping Lu, Lujia Zhang","doi":"10.1093/database/baaf001","DOIUrl":"10.1093/database/baaf001","url":null,"abstract":"Enzymes, serving as eco-friendly catalysts, are progressively supplanting traditional chemical catalysts in light industry sectors such as feed, papermaking, textiles, detergents, leather, and sugar production. Despite this advancement, the variability in the performance of natural enzymes and the fragmentation and diversity of existing data formats pose significant challenges to researchers. Furthermore, AI-driven enzyme design is limited by the quality and quantity of available data. To address these issues, we introduce the light industrial core enzyme database (LICEDB), the first database dedicated exclusively to managing and standardizing enzymes for light industry applications. LICEDB, with its integrated modules for data retrieval, similarity analysis, and structural analysis, will enhance the efficient industrial application of enzymes and strengthen AI-driven predictive research, thereby advancing data sharing and utilization in the field of enzyme innovation. Database URL: http://lujialab.org.cn/on-line-databases/.","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11842304/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143467293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design. LICEDB：用于工业应用和AI酶设计的轻工业核心酶数据库。

IF 3.4 4区生物学

Database: The Journal of Biological Databases and Curation Pub Date : 2025-02-19 DOI: 10.1093/database/baaf001

Lei Gong, Fufeng Liu, Chuanxi Zhang, Yongfan Ming, Yulan Mou, ZhaoTing Yuan, Haiming Jiang, Bei Gao, Fuping Lu, Lujia Zhang

{"title":"LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design.","authors":"Lei Gong, Fufeng Liu, Chuanxi Zhang, Yongfan Ming, Yulan Mou, ZhaoTing Yuan, Haiming Jiang, Bei Gao, Fuping Lu, Lujia Zhang","doi":"10.1093/database/baaf001","DOIUrl":"https://doi.org/10.1093/database/baaf001","url":null,"abstract":"Enzymes, serving as eco-friendly catalysts, are progressively supplanting traditional chemical catalysts in light industry sectors such as feed, papermaking, textiles, detergents, leather, and sugar production. Despite this advancement, the variability in the performance of natural enzymes and the fragmentation and diversity of existing data formats pose significant challenges to researchers. Furthermore, AI-driven enzyme design is limited by the quality and quantity of available data. To address these issues, we introduce the light industrial core enzyme database (LICEDB), the first database dedicated exclusively to managing and standardizing enzymes for light industry applications. LICEDB, with its integrated modules for data retrieval, similarity analysis, and structural analysis, will enhance the efficient industrial application of enzymes and strengthen AI-driven predictive research, thereby advancing data sharing and utilization in the field of enzyme innovation. Database URL: http://lujialab.org.cn/on-line-databases/.","PeriodicalId":10923,"journal":{"name":"Database: The Journal of Biological Databases and Curation","volume":"2025 ","pages":""},"PeriodicalIF":3.4,"publicationDate":"2025-02-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144126869","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0