Database Pub Date : 2022-03-09 DOI: 10.1093/database/baac003

Nan Deng, Canglin Wu, A. Yaseen, Hulin Wu

{"title":"ImmuneData: an integrated data discovery system for immunology data repositories","authors":"Nan Deng, Canglin Wu, A. Yaseen, Hulin Wu","doi":"10.1093/database/baac003","DOIUrl":"https://doi.org/10.1093/database/baac003","url":null,"abstract":"To meet the increasing demand for data sharing, data reuse and meta-analysis in the immunology research community, we have developed the data discovery system ImmuneData. The system provides integrated access to five immunology data repositories funded by the National Institute of Allergy and Infectious Diseases, Division of Allergy, Immunology and Transplantation, including ImmPort, ImmuneSpace, ITN TrialShare, ImmGen and IEDB. ImmuneData restructures the data repositories' metadata into a uniform schema using domain experts' knowledge and state-of-the-art Natural Language Processing (NLP) technologies. It comes with a user-friendly web interface, accessible at http://www.immunedata.org/, and a Google-like search engine for biological researchers to find and access data easily. The vast quantity of synonyms used in biomedical research increase the likelihood of incomplete search results. Thus, our search engine converts queries submitted by users into ontology terms, which are then expended by NLP technologies to ensure that the search results will include all synonyms for a particular concept. The system also includes an advanced search function to build customized queries to meet higher-level users' needs. ImmuneData ensures the FAIR principle (Findability, Accessibility, Interoperability and Reusability) of the five data repositories to benefit data reuse in the immunology research community. The data pipeline constructing our system can be extended to other data repositories to build a more comprehensive biological data discovery system.\u0000\u0000\u0000DATABASE URL\u0000http://www.immunedata.org/.","PeriodicalId":81074,"journal":{"name":"Database","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61078046","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank 快速自动验证，注释和发布SARS-CoV-2序列到GenBank

Database Pub Date : 2022-03-01 DOI: 10.1093/database/baac006

Beverly A. Underwood, L. Yankie, Eric P. Nawrocki, Vasuki Palanigobu, Sergiy Gotvyanskyy, V. C. Calhoun, Michael Kornbluh, Thomas G. Smith, Lydia Fleischmann, D. Sinyakov, Colleen J. Bollin, I. Karsch-Mizrachi

{"title":"Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank","authors":"Beverly A. Underwood, L. Yankie, Eric P. Nawrocki, Vasuki Palanigobu, Sergiy Gotvyanskyy, V. C. Calhoun, Michael Kornbluh, Thomas G. Smith, Lydia Fleischmann, D. Sinyakov, Colleen J. Bollin, I. Karsch-Mizrachi","doi":"10.1093/database/baac006","DOIUrl":"https://doi.org/10.1093/database/baac006","url":null,"abstract":"Rapid response to the current coronavirus disease 2019 (COVID-19) pandemic requires fast dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic sequence data in order to align diagnostic tests and vaccines with the natural evolution of the virus as it spreads through the world. To facilitate this, the National Library of Medicine's National Center for Biotechnology Information developed an automated pipeline for the deposition and quick processing of SARS-CoV-2 genome assemblies into GenBank for the user community. The pipeline ensures the collection of contextual information about the virus source, assesses sequence quality and annotates descriptive biological features, such as protein-coding regions and mature peptides. The process promotes standardized nomenclature and creates and publishes fully processed GenBank files within minutes of deposition. The software has processed and published 982 454 annotated SARS-CoV-2 sequences, as of 21 October 2021. This development addresses the needs of the scientific community as the sequencing of SARS-CoV-2 genomes increases and will facilitate unrestricted access to and usability of SARS-CoV-2 genomic sequence data, providing important reagents for scientific and public health activities in response to the COVID-19 pandemic. Database URL https://submit.ncbi.nlm.nih.gov/sarscov2/genbank/.","PeriodicalId":81074,"journal":{"name":"Database","volume":"2022 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"61078549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

OUP accepted manuscript OUP接受稿件

Database Pub Date : 2022-01-01 DOI: 10.1093/database/baac013

引用次数: 0

OUP accepted manuscript OUP接受稿件

Database Pub Date : 2022-01-01 DOI: 10.1093/database/baac024

引用次数: 0

OUP accepted manuscript OUP接受稿件

Database Pub Date : 2022-01-01 DOI: 10.1093/database/baac033

引用次数: 0

Design of a Software Tool for Privacy-Preserving Data Publishing 一个保护隐私的数据发布软件工具的设计

Database Pub Date : 2014-12-19 DOI: 10.14257/ASTL.2014.65.14

S. Jang

引用次数: 1

Extended Approach for the 2-Phase Query Evaluation (2PE) Scheme 两阶段查询评估(2PE)方案的扩展方法

Database Pub Date : 2014-12-19 DOI: 10.14257/ASTL.2014.65.12

Hyun-Ho Lee, H. Park, Jin-Chul Park, K. Joo

{"title":"Extended Approach for the 2-Phase Query Evaluation (2PE) Scheme","authors":"Hyun-Ho Lee, H. Park, Jin-Chul Park, K. Joo","doi":"10.14257/ASTL.2014.65.12","DOIUrl":"https://doi.org/10.14257/ASTL.2014.65.12","url":null,"abstract":"Based on the previously proposed 2PE scheme, this paper proposes a new scheme called a 2-Phase Multiple Query Evaluation (2PME). The proposed scheme extends the 2PE scheme in a way that enables multiple multi- way join continuous queries to be more efficiently processed. It constructs a global execution plan that clusters a common sub-query walk (SQW) shared by more than two queries. Each cluster is executed only one time instead of being executed repeatedly for every related query. Ongoing changes in the rapid data streams in a data stream management system (DSMS) may be monitored using a number of pre-registered queries that report results continuously as new data elements of the data streams arrive (1,2). These queries are called continuous queries. In a previous study, we proposed a 2-phase query evaluation (2PE) scheme for a single multi-way join continuous query. Given a continuous query over multiple data streams, a preprocessing phase detects whether newly arrived stream tuples satisfy the query by identifying the maximum number of candidate tuples that could satisfy it. Subsequently, a evaluation phase identifies the stream tuples that satisfy the query among the candidate tuples specified in the previous phase. In this paper, the proposed 2PE scheme is extended as a way to process multiple continuous queries. It is called a 2-phase multiple query evaluation (2PME) scheme. Given a multi-way join continuous query, the 2PE scheme has defined a query walk, which is a specific order in which all the join predicates of the query are processed. The main issue of the 2PME scheme is how to efficiently share the common sub-query walks among the multiple multi-way join continuous queries, based on the matrix-based approach of 2PE. The proposed scheme shares common sub-query walks by constructing a global execution plan where the sub-query walks that are applicable to more than two continuous queries are clustered. Each cluster is","PeriodicalId":81074,"journal":{"name":"Database","volume":"1 1","pages":"49-53"},"PeriodicalIF":0.0,"publicationDate":"2014-12-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"66977950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Analysis of Smoking in Korean Adolescents Based on Data Mining Techniques 基于数据挖掘技术的韩国青少年吸烟分析

Database Pub Date : 2014-12-19 DOI: 10.14257/ASTL.2014.65.13

H. Byeon, Rae-ho Lee

引用次数: 0

Performance Comparison of GPUs with a Genetic Algorithm based on CUDA 基于CUDA遗传算法的gpu性能比较

Database Pub Date : 2014-12-19 DOI: 10.14257/ASTL.2014.65.09

Jae-Hyun Seo, Eun-Sol Ko, Yong-Hyuk Kim

引用次数: 2

Word Sense Disambiguation Using Tree-based Association Rule 基于树的关联规则的词义消歧

Database Pub Date : 2014-12-19 DOI: 10.14257/ASTL.2014.65.10

Jung-Gil Cho, Won-Whoi Huh