期刊文献+
共找到234篇文章
< 1 2 12 >
每页显示 20 50 100
Restauro-G:A Rapid Genome Re-Annotation System for Comparative Genomics 被引量:1
1
作者 Satoshi Tamaki Kazuharu Arakawa +1 位作者 Nobuaki Kono Masaru Tomita 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2007年第1期53-58,共6页
of complete genome sequences submitted directly from sequencing projects are diverse in terms of annotation strategies and update frequencies. These inconsistencies make comparative studies difficult. To allow rapid d... of complete genome sequences submitted directly from sequencing projects are diverse in terms of annotation strategies and update frequencies. These inconsistencies make comparative studies difficult. To allow rapid data preparation of a large number of complete genomes, automation and speed are important for genome re-annotation. Here we introduce an open-source rapid genome re-annotation software system, Restauro-G, specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLASTLike Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases. Restauro-G was developed in the generic bioinformatics workbench G-language Genome Analysis Environment and is distributed at http://restauro-g.iab.keio.ac.jp/ under the GNU General Public License. 展开更多
关键词 BIOINFORMATICS SOFTWARE annotation G-language Genome Analysis Environment complete genomes
在线阅读 下载PDF
Systematic identification and annotation of multiple-variant compound effects at transcription factor binding sites in human genome 被引量:1
2
作者 Si-Jin Cheng Shuai Jiang +2 位作者 Fang-Yuan Shi Yang Ding Ge Gao 《Journal of Genetics and Genomics》 SCIE CAS CSCD 2018年第7期373-379,共7页
Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites (TFBSs) are one of the most important cis-regulatory elements. While multiple t... Understanding the functional effects of genetic variants is crucial in modern genomics and genetics. Transcription factor binding sites (TFBSs) are one of the most important cis-regulatory elements. While multiple tools have been developed to assess functional effects of genetic variants at TFBSs, they usually assume that each variant works in isolation and neglect the potential "interference" among multiple variants within the same TFBS. In this study, we presented COPE-TFBS (Context-Oriented Predictor for variant Effect on Transcription Factor Binding Site), a novel method that considers sequence context to accurately predict variant effects on TFBSs. We systematically re-analyzed the sequencing data from both the 1000 Genomes Project and the Genotype-Tissue Expression (GTEx) Project via COPE-TFBS, and identified numbers of novel TFBSs, transformed TFBSs and discordantly annotated TFBSs resulting from multiple variants, further highlighting the necessity of sequence context in accurately annotating genetic variants. 展开更多
关键词 Compound effect Transcription factor binding site Variant annotation BIOINFORMATICS Genetic variants
原文传递
Medical Entity and Attributes Extraction System Based on Relation Annotation 被引量:1
3
作者 ZOU Yuwei GU Jinguang FU Haidong 《Wuhan University Journal of Natural Sciences》 CAS CSCD 2016年第2期145-150,共6页
The abundant entities and entity-attribute relations in medical websites are important data resources for medical research.However,the medical websites are usually characterized of storing entity and attribute values ... The abundant entities and entity-attribute relations in medical websites are important data resources for medical research.However,the medical websites are usually characterized of storing entity and attribute values in different pages.To extract those data records efficiently,we propose an automatic extraction system which is related to entity and attribute relations(attributes and values)of separate storage.Our system includes following modules:(1)rich-information interactive annotation page rendering;(2)separate storage attribute relations annotating;(3)annotated relations for pattern generating and data records extracting.This paper presents the relations about the attributes which are stored in many pages by effective annotation,then generates rules for data records extraction.The experiments show that the system can not only complete attribute relations of separate storage extraction,but also be compatible with regular relation extraction,while maintaining high accuracy. 展开更多
关键词 relation annotation information extraction medical data relation extraction
原文传递
Guidelines for glaucoma imaging classification,annotation,and quality control for artificial intelligence applications
4
作者 Wei-Hua Yang Yan-Wu Xu +3 位作者 Xing-Huai Sun Expert Workgroup of Guidelines for Glaucoma Imaging Classification Annotation Quality Control for Artificial Intelligence Applications 《International Journal of Ophthalmology(English edition)》 2025年第7期1181-1196,共16页
Glaucoma is an eye disease characterized by pathologically elevated intraocular pressure,optic nerve atrophy,and visual field defects,which can lead to irreversible vision loss.In recent years,the rapid development of... Glaucoma is an eye disease characterized by pathologically elevated intraocular pressure,optic nerve atrophy,and visual field defects,which can lead to irreversible vision loss.In recent years,the rapid development of artificial intelligence(AI)technology has provided new approaches for the early diagnosis and management of glaucoma.By classifying and annotating glaucoma-related images,AI models can learn and recognize the specific pathological features of glaucoma,thereby achieving automated imaging analysis and classification.Research on glaucoma imaging classification and annotation mainly involves color fundus photography(CFP),optical coherence tomography(OCT),anterior segment optical coherence tomography(AS-OCT),and ultrasound biomicroscopy(UBM)images.CFP is primarily used for the annotation of the optic cup and disc,while OCT is used for measuring and annotating the thickness of the retinal nerve fiber layer,and AS-OCT and UBM focus on the annotation of the anterior chamber angle structure and the measurement of anterior segment structural parameters.To standardize the classification and annotation of glaucoma images,enhance the quality and consistency of annotated data,and promote the clinical application of intelligent ophthalmology,this guideline has been developed.This guideline systematically elaborates on the principles,methods,processes,and quality control requirements for the classification and annotation of glaucoma images,providing standardized guidance for the classification and annotation of glaucoma images. 展开更多
关键词 GLAUCOMA ar tificial intelligence classification annotation PROCESSES quality control GUIDELINE
原文传递
Mass spectral database-based methodologies for the annotation and discovery of natural products
5
作者 Fengyao Yang Zeyuan Liang +4 位作者 Haoran Zhao Jiayi Zheng Lifang Liu Huipeng Song Guizhong Xin 《Chinese Journal of Natural Medicines》 2025年第4期410-420,共11页
Natural products(NPs)have long held a significant position in various fields such as medicine,food,agriculture,and materials.The chemical space covered by NPs is extensive but often underexplored.Therefore,high-throug... Natural products(NPs)have long held a significant position in various fields such as medicine,food,agriculture,and materials.The chemical space covered by NPs is extensive but often underexplored.Therefore,high-throughput and efficient methodologies for the annotation and discovery of NPs are desired to address the complexity and diversity of NP-based systems.Mass spectrometry(MS)has emerged as a powerful platform for the annotation and discovery of NPs.MS databases provide vital support for the structural characterization of NPs by integrating extensive mass spectral data and sample information.Additionally,the released annotation methodologies,based on a variety of informatics tools,continuously improve the ability to annotate the structure and properties of compounds.This review examines the current mainstream databases and annotation methodologies,focusing on their advantages and limitations.Prospects for future technological advancements are then discussed in terms of novel applications and research objectives.Through a systematic overview,this review aims to provide valuable insights and a reference for MS-based NPs annotation,thereby promoting the discovery of novel natural entities. 展开更多
关键词 Mass spectrometry Natural products annotation DATABASES
原文传递
Annotation and assessment of functional variants in livestock through epigenomic data
6
作者 Ruixian Ma Renzhuo Kuang +14 位作者 Jingcheng Zhang Jiahao Sun Yueyuan Xu Xinbo Zhou Zheyu Han Mingyang Hu Daoyuan Wang Yuhua Fu Yong Zhang Xinyun Li Mengjin Zhu Shuhong Zhao Tao Xiang Mengwei Shi Yunxia Zhao 《Journal of Genetics and Genomics》 2025年第12期1588-1599,共12页
Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding.However,the lack of comprehensive functional genomic annotations in animals limits the effectiveness of mos... Understanding genetic variant functionality is essential for advancing animal genomics and precision breeding.However,the lack of comprehensive functional genomic annotations in animals limits the effectiveness of most variant function assessment methods.In this study,we gather 1030 raw epigenomic datasets from 10 animal species and systematically annotate 7 types of key regulatory regions,creating a comprehensive functional annotation map of animal genomic variants.Our findings demonstrate that integrating variants with regulatory annotations can identify tissues and cell types underlying economic traits,underscoring the utility of these annotations in functional variant discovery.Using our functional annotations,we rank the functional potential of genetic variants and classify over 127 million candidate variants into 5 functional confidence categories,with high-confidence variants significantly enriched in eQTLs and trait-associated SNPs.Incorporating these variants into genomic prediction models can improve estimated breeding value accuracy,demonstrating their practical utility in breeding programs.To facilitate the use of our results,we develop the Integrated Functional Mutation(IFmut:http://www.ifmutants.com:8212)platform,enabling researchers to explore regulatory annotations and assess the functional potential of animal variants efficiently.Our study provides a robust framework for functional genomic annotations in farm animals,enhancing variant function assessment and breeding precision. 展开更多
关键词 Epigenetic annotation Functional variants assessment Estimated breeding values(EBVs) Functional mutation database
原文传递
基于Annotation的Spring AOP系统设计 被引量:7
7
作者 刘荣辉 薛冰 《计算机应用与软件》 CSCD 2009年第9期18-20,共3页
简要介绍AOP(Aspect Oriented Programming)技术和Annotation技术,讨论了Spring中的AOP的两种实现。通过同一个案例阐述了在Spring中通过XML配置来实现AOP和使用了Annotation在Spring中实现AOP,比较了两种实现方式的优缺点。对在Spring... 简要介绍AOP(Aspect Oriented Programming)技术和Annotation技术,讨论了Spring中的AOP的两种实现。通过同一个案例阐述了在Spring中通过XML配置来实现AOP和使用了Annotation在Spring中实现AOP,比较了两种实现方式的优缺点。对在Spring使用Annotation实现AOP作了总结,从而体现了Annotation在设计系统时其简洁性和良好的扩展性。 展开更多
关键词 SPRING XML AOP annotation
在线阅读 下载PDF
基于XML和Annotation的异构系统数据集成方式的研究 被引量:2
8
作者 肖刚 《计算机与数字工程》 2014年第6期1019-1022,1082,共5页
论文运用XML的强大数据表达能力以及J2EE的反射以及Annotation编程来实现异构系统数据集成方式。该方式通过对原始结构代码进行简单的标记,将不同的数据结构串联起来。同时在转换的过程中将细节屏蔽起来并封装成标准接口,用户只需要将... 论文运用XML的强大数据表达能力以及J2EE的反射以及Annotation编程来实现异构系统数据集成方式。该方式通过对原始结构代码进行简单的标记,将不同的数据结构串联起来。同时在转换的过程中将细节屏蔽起来并封装成标准接口,用户只需要将提供输入以及所需要的数据结构类型就可以方便地进行转换。最后论文给出集成系统详细的设计方法。 展开更多
关键词 XML语言 annotation编程 数据集成 异构系统
在线阅读 下载PDF
Product image sentence annotation based on kernel descriptors and tag-rank
9
作者 张红斌 姬东鸿 +2 位作者 尹兰 任亚峰 殷依 《Journal of Southeast University(English Edition)》 EI CAS 2016年第2期170-176,共7页
Dealing with issues such as too simple image features and word noise inference in product image sentence anmotation, a product image sentence annotation model focusing on image feature learning and key words summariza... Dealing with issues such as too simple image features and word noise inference in product image sentence anmotation, a product image sentence annotation model focusing on image feature learning and key words summarization is described. Three kernel descriptors such as gradient, shape, and color are extracted, respectively. Feature late-fusion is executed in turn by the multiple kernel learning model to obtain more discriminant image features. Absolute rank and relative rank of the tag-rank model are used to boost the key words' weights. A new word integration algorithm named word sequence blocks building (WSBB) is designed to create N-gram word sequences. Sentences are generated according to the N-gram word sequences and predefined templates. Experimental results show that both the BLEU-1 scores and BLEU-2 scores of the sentences are superior to those of the state-of-art baselines. 展开更多
关键词 product image sentence annotation kerneldescriptors tag-rank word sequence blocks building(WSBB) N-gram word sequences
在线阅读 下载PDF
Detecting abnormalities for empty nest elder in smart monitoring system
10
作者 杨蕾 杨路明 +1 位作者 满君丰 刘广滨 《Journal of Southeast University(English Edition)》 EI CAS 2008年第3期347-350,共4页
In order to implement the real-time detection of abnormality of elder and devices in an empty nest home,multi-modal joint sensors are used to collect discrete action sequences of behavior,and the improved hierarchical... In order to implement the real-time detection of abnormality of elder and devices in an empty nest home,multi-modal joint sensors are used to collect discrete action sequences of behavior,and the improved hierarchical hidden Markov model is adopted to Abstract these discrete action sequences captured by multi-modal joint sensors into an occupant’s high-level behavior—event,then structure representation models of occupant normality are modeled from large amounts of spatio-temporal data. These models are used as classifiers of normality to detect an occupant’s abnormal behavior.In order to express context information needed by reasoning and detection,multi-media ontology (MMO) is designed to annotate and reason about the media information in the smart monitoring system.A pessimistic emotion model (PEM) is improved to analyze multi-interleaving events of multi-active devices in the home.Experiments demonstrate that the PEM can enhance the accuracy and reliability for detecting active devices when these devices are in blind regions or are occlusive. The above approach has good performance in detecting abnormalities involving occupants and devices in a real-time way. 展开更多
关键词 multi-media ontology semantic annotation abnormality detection hierarchical hidden Markov model pessimistic emotion model
在线阅读 下载PDF
基于Annotation的Spring AOP日志处理的设计与实现 被引量:4
11
作者 张文胜 《价值工程》 2012年第32期207-209,共3页
系统维护和错误排查需要程序能自动的输出日志信息,将用户的操作记录下来。而日志本身不太可能是你开发的主程序的主要任务。如果能将"不可见的"、通用的日志代码注入主程序中,而保证自身业务逻辑的纯洁性,降低代码之间的耦合... 系统维护和错误排查需要程序能自动的输出日志信息,将用户的操作记录下来。而日志本身不太可能是你开发的主程序的主要任务。如果能将"不可见的"、通用的日志代码注入主程序中,而保证自身业务逻辑的纯洁性,降低代码之间的耦合度,增加程序的灵活性和可重用性。本文使用Spring AOP的Annotation方式,写一个切面,并且指定切入的范围(切入点),当系统运行后,日志信息将可以自动输出或记录在指定的文件及数据库中。 展开更多
关键词 面向切面编程(AOP) annotation 耦合度
在线阅读 下载PDF
基于Annotation的Spring事务应用设计
12
作者 刘荣辉 《电脑学习》 2009年第3期119-120,共2页
本文简要介绍Spring的事务实现技术,讨论了Spring中的事务的两种实现方式。通过同一个案例阐述了在Spring中通过xml配置来实现事务和使用了Annotation实现事务,比较了两种实现方式的优缺点。
关键词 SPRING XML 事务 annotation
在线阅读 下载PDF
基于Annotation数据结构自动生成的研究与实现 被引量:1
13
作者 王雪梅 李彩虹 +1 位作者 慕富强 李廉 《微电子学与计算机》 CSCD 北大核心 2017年第1期114-118,共5页
为了使整个数据库设计更加工程化、规范化和便捷化,使用Annotation注解技术实现数据库物理结构的自动生成,使之从数据库设计文档自动生成关系型数据库结构代码的方法,从而大大缩减了相关数据库开发的周期,提高了数据库开发的效率.
关键词 数据库结构 自动生成 annotation JAVA反射
在线阅读 下载PDF
用Annotation简化Java程序的开发 被引量:2
14
作者 杨宇仙 杨志勇 《计算机与现代化》 2008年第6期121-122,126,共3页
简要介绍了Annotation技术本身的实现原理,并通过具体实例阐述了如何在软件开发中使用Annotation技术来简化Java程序开发的复杂性,提高程序的可读性和易用性。同时归纳了Annotation技术与XML技术各自的优缺点及适用范围。
关键词 JAVA annotation XML 元数据
在线阅读 下载PDF
基于Annotation的Spring事务应用设计 被引量:2
15
作者 刘荣辉 《微型电脑应用》 2009年第7期57-59,6,共3页
该文简要介绍Spring的事务实现技术,讨论了Spring中的事务的两种实现方式。通过同一个案例阐述了在Spring中通过xml配置来实现事务和使用了Annotation实现事务,比较了两种实现方式的优缺点。对在Spring使用Annotation实现事务作了总结,... 该文简要介绍Spring的事务实现技术,讨论了Spring中的事务的两种实现方式。通过同一个案例阐述了在Spring中通过xml配置来实现事务和使用了Annotation实现事务,比较了两种实现方式的优缺点。对在Spring使用Annotation实现事务作了总结,从而体现使用Annotation实现事务简洁性和良好的扩展性。 展开更多
关键词 SPRING XML 事务 annotation
在线阅读 下载PDF
Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing 被引量:13
16
作者 Mao-Sen Ye Jin-Yan Zhang +6 位作者 Dan-Dan Yu Min Xu Ling Xu Long-Bao Lv Qi-Yun Zhu Yu Fan Yong-Gang Yao 《Zoological Research》 SCIE CAS CSCD 2021年第6期692-709,共18页
The Chinese tree shrew(Tupaia belangeri chinensis)is emerging as an important experimental animal in multiple fields of biomedical research.Comprehensive reference genome annotation for both mRNA and long non-coding R... The Chinese tree shrew(Tupaia belangeri chinensis)is emerging as an important experimental animal in multiple fields of biomedical research.Comprehensive reference genome annotation for both mRNA and long non-coding RNA(lncRNA)is crucial for developing animal models using this species.In the current study,we collected a total of 234 high-quality RNA sequencing(RNA-seq)datasets and two long-read isoform sequencing(ISO-seq)datasets and improved the annotation of our previously assembled high-quality chromosomelevel tree shrew genome.We obtained a total of 3514 newly annotated coding genes and 50576 lncRNA genes.We also characterized the tissuespecific expression patterns and alternative splicing patterns of mRNAs and lncRNAs and mapped the orthologous relationships among 11 mammalian species using the current annotated genome.We identified 144 tree shrew-specific gene families,including interleukin 6(IL6)and STT3 oligosaccharyltransferase complex catalytic subunit B(STT3B),which underwent significant changes in size.Comparison of the overall expression patterns in tissues and pathways across four species(human,rhesus monkey,tree shrew,and mouse)indicated that tree shrews are more similar to primates than to mice at the tissue-transcriptome level.Notably,the newly annotated purine rich element binding protein A(PURA)gene and the STT3B gene family showed dysregulation upon viral infection.The updated version of the tree shrew genome annotation(KIZ version 3:TS_3.0)is available at http://www.treeshrewdb.org and provides an essential reference for basic and biomedical studies using tree shrew animal models. 展开更多
关键词 Tree shrew Genome annotation TRANSCRIPTOME Gene family Virus infection
在线阅读 下载PDF
A Method of Gene-Function Annotation Based on Variable Precision Rough Sets 被引量:5
17
作者 Zhi-li Pei Xiao-hu Shi +4 位作者 Meng Niu Xu-ning Tang Li-sha Liu Ying Kong Yan-chun Liang 《Journal of Bionic Engineering》 SCIE EI CSCD 2007年第3期177-184,共8页
It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotat... It is very important in the field of bioinformatics to apply computer to perform the function annotation for new sequenced bio-sequences. Based on GO database and BLAST program, a novel method for the function annotation of new biological sequences is presented by using the variable-precision rough set theory. The proposed method is applied to the real data in GO database to examine its effectiveness. Numerical results show that the proposed method has better precision, recall-rate and harmonic mean value compared with existing methods. 展开更多
关键词 gene function annotation variable precision rough set GO BLAST
在线阅读 下载PDF
Author Correction:Updated annotation of the wild strawberry Fragaria vesca V4 genome 被引量:5
18
作者 Yongping Li Mengting Pi +2 位作者 Qi Gao Zhongchi Liu Chunying Kang 《Horticulture Research》 SCIE 2019年第1期704-704,共1页
Since the publication of this article,the authors have noticed that the GeneIDs from new and original genome annotations don’t match in Table S6,the correct Table S6 is given here.The authors would like to apologize ... Since the publication of this article,the authors have noticed that the GeneIDs from new and original genome annotations don’t match in Table S6,the correct Table S6 is given here.The authors would like to apologize for this error. 展开更多
关键词 FRAGARIA STRAW annotation
原文传递
Automatic"Ground Truth"Annotation and Industrial Workpiece Dataset Generation for Deep Learning 被引量:3
19
作者 Fu-Qiang Liu Zong-Yi Wang 《International Journal of Automation and computing》 EI CSCD 2020年第4期539-550,共12页
In industry,it is becoming common to detect and recognize industrial workpieces using deep learning methods.In this field,the lack of datasets is a big problem,and collecting and annotating datasets in this field is v... In industry,it is becoming common to detect and recognize industrial workpieces using deep learning methods.In this field,the lack of datasets is a big problem,and collecting and annotating datasets in this field is very labor intensive.The researchers need to perform dataset annotation if a dataset is generated by themselves.It is also one of the restrictive factors that the current method based on deep learning cannot expand well.At present,there are very few workpiece datasets for industrial fields,and the existing datasets are generated from ideal workpiece computer aided design(CAD)models,for which few actual workpiece images were collected and utilized.We propose an automatic industrial workpiece dataset generation method and an automatic ground truth annotation method.Included in our methods are three algorithms that we proposed:a point cloud based spatial plane segmentation algorithm to segment the workpieces in the real scene and to obtain the annotation information of the workpieces in the images captured in the real scene;a random multiple workpiece generation algorithm to generate abundant composition datasets with random rotation workpiece angles and positions;and a tangent vector based contour tracking and completion algorithm to get improved contour images.With our procedures,annotation information can be obtained using the algorithms proposed in this paper.Upon completion of the annotation process,a json format file is generated.Faster R-CNN(Faster R-convolutional neural network),SSD(single shot multibox detector)and YOLO(you only look once:unified,real-time object detection)are trained using the datasets proposed in this paper.The experimental results show the effectiveness and integrity of this dataset generation and annotation method. 展开更多
关键词 Deep learning dataset generation automatic annotation neural networks industrial workpiece dataset
原文传递
Automatic Placement of GIS Vector Map Annotation in Area Feature by Long Diagonal 被引量:2
20
作者 LAN Xiaoji JIANG Yongfa +1 位作者 Lü Guonian DENG Huamei 《Geo-Spatial Information Science》 2005年第4期276-281,共6页
This paper discusses the placement of Chinese annotation from point of view of graphics. Area Feature is classified as simple polygon, complex polygon and special polygon. For simple ones, annotations are placed along... This paper discusses the placement of Chinese annotation from point of view of graphics. Area Feature is classified as simple polygon, complex polygon and special polygon. For simple ones, annotations are placed along the longest edge. For complex ones, firstly the polygon are simplified according to close points, then the longest diagonal is gotten by comparing length, lastly, annotations are placed along long diagonal. For special ones, the polygon are partitioned into several parts by a certain rule for getting their sub\|diagonals, then their annotation are placed by means of the second. 展开更多
关键词 long-diagonal area eature annotation automatic placement
在线阅读 下载PDF
上一页 1 2 12 下一页 到第
使用帮助 返回顶部