PubMed中文使用手册

合集下载

参考文献著录途径和查找方式

参考文献著录途径和查找方式
请作者尽量参考引用近5年的文献，以增强时效性；建议多参考引用我刊相关文章，便于提高我刊的影响力。

一、中文文献建议在以下网站搜索
1.我刊平台：通过首页上的期刊查询或关键词查询相关文章
2.百度：http://*************/
3知网：http://************/
4.万方：http://********************/
5.维普：http://*************/
二、英文文献建议在以下网站搜索：
1.Pubmed：http://********************/pubmed/
2.谷歌：http://***************
检索文献时可使用文章关键词，如“组织多普勒衍生新技术评价肥厚型心肌病心房局部功能的研究”，检索关键词可使用组织多普勒、肥厚型心肌病、心房。

文后参考文献录入标准
1.专著
编著者.题名.出版地：出版者，出版年：引文页码.
如：周永昌，郭万学.超声医学.4版.北京：科学技术文献出版社，2002:1020-1022.
Benirschke N.人类胎盘病理学手册.刘伯宁，译.天津：天津科技翻译出版公司，2008:198-199.。

如何使用PUBMED---PPT课件

与近似的主题词匹配作为文本词(自由词)检索在这种情况下,输入的检索词也将在标题和文摘中检索
作用
将不规范的词语转换成规范的用词对主题词进行
自动扩展检索这种处理能使检索结果更精确和全面。
期刊转换表
刊名全称 MEDLINE 刊名缩写 ISSN号
著者全名转换表
2002年以后发表的带有作者全名的文章作者姓名可以采用正常的或倒置的如:julia s wong wong julia s wong, julia s
预览/索引Preview/Index
Preview(预览)可以在显示条目之前显示所查到的文献数通过增加一个或多个单词来修改查询方案。向下滚动Preview/Index找到“Add to Query or View Index”部分，使用下拉菜单确定一个搜索域，向文本框中加入词语，单击 Preview可以看到查询结果。 Preview自动使用“AND”运算符来将单词合为一体，即要求同时查询包含两个词的文献显示最近三个检索式
著者索引
姓在前,名在后,名字缩写 o’brien jm adams sh pogonka t
如果在6个转换表中都没有
把词组分开重复进行自动匹配直到找到匹配词为止。如果还没有找到匹配词系统将把单个词用逻辑”与”组配并到所有字段中检索。
single cell
("single person"[MeSH Terms] OR ("single"[All Fields] AND "person"[All Fields]) OR "single person"[All Fields] OR "single"[All Fields]) AND ("cells"[MeSH Terms] OR "cells"[All Fields] OR "cell"[All Fields])

EPOCH 基本使用手册说明书

EPOCH Basic User GuideWhat is EPOCH?EPOCH is the ePortal for Online Clinical Help that gives health practitioners, ancillary staff and students working for the Tasmanian public health service online access to high-quality health and social care information resources and the clinical evidence base to support decision-making, service planning, education and research.Resources include:•medicines information•point-of-care tools•clinical guidelines and standards•electronic journals and textbooks•research databases•specialty guidesWhere is EPOCH located?EPOCH is directly available at .auAn EPOCH link is also available:•On each Department-networked computer desktop•From Shortcuts & Applications drop-down list on the Department/Tasmanian Heath Services intranet homepage at .au/intranetEPOCH registration and loginRegistration is NOT required for staff with work email addresses ending:•@.au•@.au•@.auOther users must register for EPOCH access at .au/registration-formHow do I search EPOCH?There are search and browse options at the top of EPOCH’s homepage .About Quick Search and Advanced Search options1. Quick Search Everything optionUse Quick Search Everything for a basic, exploratory search across multiple EPOCH resources and the health and care evidence.2. Quick Search drop-down menuQuick Search offers the default Everything option and four additional options for finding resources and research: 1. EverythingThe default keyword search for finding known EPOCH resources, or locating journal articles, journals, book chapters and books2. eBooksKeyword search for Department-licensed online books only3. DOI LookupTargeted search for an article or book chapter with a known “Digital Object Identifier” (DOI)4. PubMedKeyword search in largest database of biomedical research5. Google ScholarKeyword search for scholarly literature, outside EPOCH on the open web3. Advanced SearchUse Advanced Search for a more precise and detailed search. It offers features that help locate more relevant results, including:• Predicts your search terms and offers additional related terms • Pre-limits your search to include specific types of literature • Pre-limits your search to exclude literature you do not wantResults page for Quick Search Everything and Advanced Search1. MyEBSCO loginPersonalise your search session by logging into your MyEBSCO account. All EPOCH users have a MyEBSCO account to save work.2. MyEBSCO dashboardCreate projects, as well ascollect, organise and save items you find and searches you use in EPOCH search sessions. Read EPOCH’s MyEBSCODashboard User Guide for more information.au/guides-tutorials/myebsco-dashboard-folder3. Search resultsList of results retrieved from your search. Links are provided when full text is available.4. Filtering or limiting searchresultsOptions for reducing your set of results by specifying a date range, a type of resource and more.5. Sorting search resultsView results by most relevant or most recent.6. Advanced SearchOption for a more precise, detailed search.7. Publication resultsWhen your search retrieves a journal or book that is part of the Department online collection.8. Featured resultsWhen your search retrieves a recommended EPOCH product or research database.More help with your searches and working with results•Video Introductionyoutu.be/glUgGoUzj5M•General Search/s/article/EBSCO-Discovery-Service-General-Search•Advanced Search/s/article/New-EBSCO-Discovery-Service-Advanced-Search •Applying Limiters and Filters to Your Search Results/s/article/Applying-Limiters-and-Filters-in-the-New-EBSCO-Interfaces •Using the Bookmark Feature/s/article/Using-the-Bookmark-Feature•Using the Cite Tool/s/article/Using-the-Cite-Tool•Your Personal Account and Dashboard.au/guides-tutorials/myebsco-dashboard-folderAbout other search and browse options4. A-Z Journal BrowseSearch or browse our collection of online journals by title, or subjects and specialties. 5. A-Z eBook BrowseSearch our collection of online books by keyword or browse across specialties andfocused collections that highlight new titles, core titles, and more.6. Library CatalogueStatewide catalogue of the Department’s print collection located at our North, North West and South Library sites. Allows staff to search, discover and request books, reports and other printed material collected and maintained by Library Services.FAQsFind quick answers related to access, authentication, troubleshooting individual resources, and other general queries at .au/faqsTraining and helpEPOCH provides a range of training options to staff for support finding health and care evidence. Visit .au/training to:•Check scheduled online training sessions•Arrange individual or group training sessions•Organise a consultation with Library ServicesContact usEPOCH Help Desk 1300 980 632NORTHSir John Ramsay Memorial Library p. (03) 6777 6056e. **************.gov.auNORTH WESTDr Richard Buttfield Libraryp. (03) 6493 6043e. *************************.gov.au SOUTHWingfield Libraryp. (03) 6166 1002e. ***************.gov.auRoyal Hobart Hospital Library Kiosk m. 0436 635 298Department of Health GPO Box 125Hobart TAS 7001 1300 135 513.au。

Cn3D 4.1中文使用手册

Cn3D 4.1中文使用手册Yang Xin（yx3240106@）翻译生物秀Welcome to the Cn3D 4.1 Tutorial! 目录•简介o Cn3D的基本功能o下载和安装Cn3Do文档约定o参考文献•寻找特定的结构(MMDB)o根据Entrez文献研究o根据Entrez 临近序列o通过BLAST搜索o通过已知的PDB标识•在Cn3D中察看特定的序列结构o Cn3D的基本控制操作结构窗体的主菜单样式面板o Cn3D的序列阅读器•结构比较(VAST)o在Cn3D中察看结构比较结果Cn3D的比对察看器Cn3D的比对模块•导入和保存o导入序列和空间结构o可见的序列保守性•注释结构o骨架和界标o自定义样式•保存空间结构和图像o将Cn3D用于交互式图形•高级设置o动画控制o显示无序晶体o类型搜寻o导入用户PDB文件•比对编辑o使用编辑器o校正队列错误o将序列合并到多重序列中简介这是 Cn3D 4.1的使用手册。

希望能够向初次使用或是曾经使用过Cn3D的用户提供一个关于本软件的基本特点的指导。

新用户可能希望通过阅读这篇文档来学习如何使用Cn3D,而有经验的用户则可以通过上面的目录和超连接直接跳转到自己感兴趣的章节。

本手册并不是对程序功能的详尽的介绍。

在Cn3D的安装程序里包含有关于Cn3D的用户界面和详细功能介绍的帮助文档。

—见Cn3D_Commands.chm。

Cn3D 的基本功能Cn3D 是一个生物分子的三维结构、序列以及序列比对结果的可视化工具。

Cn3D可以将结构与序列的信息紧密的联系起来，这是它与其它软件的一个重要的区别：例如，一名科学家可以很快的从晶体结构中找出与导致已知疾病的突变相关的残基，或是保留同源序列家族的活性位点的残基。

Cn3D可以通过基于结构的序列比较来显示生物分子结构之间的比较，从而了解相关蛋白的那一个结构域在结构与序列上表现得更为保守。

同时，可以自定义标签的特性，高品质的OpenGL 的画质，还有多样的文件输出格式，都使得Cn3D成为文献注释的强大工具。

PubMed使用手册

PubMed使用手册【基本查询方法】•一个检索词：一个单词：在文本框中输入检索词，按GO查询。

含两个单词以上的检索词：需要加双引号，注意是英文输入状态下的双引号。

如："ultrasonic diagnosis"是正确的，“ultrasonic diagnosis”是错误的•两个以上的检索词：可使用AND、OR 连接各检索词。

如："three dimensional ultrasound" AND thyroid •可以在“limit”菜单下限制文献出版的时间、语种等等。

【完全手册】PubMed 系统的主要特点1.词汇自动转换功能（Automatic Term Mapping）在PubMed主页的检索提问框中键入检索词，系统将按顺序使用如下4种表或索引，对检索词进行转换后再检索。

（1）MeSH转换表（MeSH Translation Table），包括MeSH词、参见词、副主题词等。

如果系统在该表中发现了与检索词相匹配的词，就会自动将其转换为相应的MeSH词和TextWord词（题名词和文摘词）进行检索。

例如：键入"Vitamin h"，系统将其转换成"Biotin [MeSH Tems] OR Vitamin h [Textword]"后进行检索。

（2）刊名转换表（Journal Tanslation Table），包括刊名全称、MEDLINE 形式的缩写和ISSN号。

该转换表能把键入的刊名全称转换为"MEDLINE缩写[Journal Name]"后进行检索。

如：在检索提问框中键入："new england journal of medicine", PubMed将其转换为"N Engl J Med [Journal Name]"后进行检索。

（3）短语表（Phrase list）。

PubMed使用教程指南

获取原文及相关资源
1.联机获取原文（ free full text article） 2. link out 3.向有关图书馆索要 4.其他数据库资源（生物信息学等）
文摘中的期刊图标链接
Linkout链接
点击获取原文
检索实例
1.哮喘的药物治疗（asthma, drug therapy） asthma/drug therapy
一、基本检索
1.词语检索
自动匹配转换.
自动匹配转换功能
主题词索引作者索引期刊索引
自动匹配转换过程.
一、基本检索 2.精确检索
强制将其作为一个词组检索
3.截词检索
一、基本检索
无限截词检索
3.截词检索
一、基本检索
有限截词检索
4.逻辑组配检索
一、基本检索
逻辑组配检索
5.作者检索
一、基本检索
Abstract :来源期刊、标题、著者、著者地址、记录性质、文献类型、勘误、评论、 PMID或UI、摘要。 Summery：作者 Citation : 显示除上述内容外，加MeSH叙词、化学物质名称、资助项目号等字段。 MEDLINE : (最完整，有标识符）
显示字段选择（Display)
PUBMED检索途径一、基本检索区二、辅助检索区三、个性化检索区
PubMed主页
基本检索区辅助检索区提供辅助检索功能
个性化检索区
一、基本检索
可对任何具有实质意义的词都可以进行检索，如: 1.词语检索自动匹配功能 2.精确检索用“ ”进行强制短语检索 3.截词检索用通配符？，*检索 4.逻辑组配检索 AND OR NOT 5.作者检索 6.期刊检索

PubMed使用指南

- 世界上权威性的生物医学书目型数据库，收录全世界范围内70多个国家和地区近5000种生物医学相关期刊论文，主要收录英语语种期刊，少部分其他语种期刊。
- 学科范围涵盖基础医学、临床医学、护理学、口腔医学、兽医学、营养卫生、药理和药剂学、预防医学、卫生管理、医疗保健和情报科学领域，2000年起新增生物、环境科学、海洋生物、植物和动物学、生物物理学和生物化学等生命科学领域
医学文献资源检索与利用
PubMed数据库检索
20 数据库检索检索结果处理ＭyNCBI
1、PubMed------概况
- 纸质版（Index Medicus,IM美国医学索引）-----光盘版（MEDLARS on Line ,MEDLINE）------网络版(PubMed)，收录时间范围：1947-，部分期刊回溯至创刊年。数据每日更新(Tuesday – Saturday)
重新执行已保存的策略
修改已保存的策略
③个性化设置
更改高亮显示颜色
PubMed小结
权威的生物医学二次文献数据库便利的全文链接即时的文献线索多样化的检索途径准确、全面的检索效率个性化检索服务
⑤. PubMed------Clinical Queries
为帮助临床医生更有效地获取PubMed数据库中一般疾病的病因学、预后、诊断、治疗及预防等方面的信息， PubMed设置了Clinical Queries功能。该功能具备特殊的过滤器装置能将上述主题文献集中提供检索。
①PubMed基本检索
- 支持布尔逻辑运算 AND, OR, NOT - 支持截词检索* - 支持字段检索：如liver cancer[ti] - 支持短语检索 “ ” - 自动词语匹配(字段限定、词组、截词检索时该功能失效)

NCBI使用手册上

The NCBI Handbookstudent will submit questions for a classroom assignment, providing a special outreach opportunity to young scientists.Because of the genetic focus of many of NCBI resources, we receive a number of questions from the general public regarding medical issues. The NCBI Help Desk staff can neither provide direct answers to medical questions nor give medical advice or guidance. However,we do provide suggestions on how to search our resources for information on the gene or condition of interest and refer users to the National Library of Medicine (NLM) customer service group for further assistance with PubMed (Chapter 2), MEDLINEplus, and . We also refer them to outside organizations that can provide information on such topics as support groups and sources of medical advice.Questions about PubMed are handled by a separate customer service group within the NLM.Their direct address is custserv@, and their phone number is 1-888-FIND-NLM.PubMed questions that are received at the NCBI Help Desk are forwarded to NLM.Development of User Support Materials Because of its ongoing personal contact with our users, the User Services group plays an important role in communicating with database development and production teams, making suggestions, testing new releases and new features, and keeping them informed of problems that people are having with the services. The team also collaborates with developers in creating help documents, frequently asked questions (FAQs), tutorials, and workshop materials.Tutorials on the Web Web-based tutorials for BLAST, Entrez, Cn3D, and PubMed are currently available, with additional topics under development. Tutorials are produced on a collaborative basis by database development and User Services staff.About NCBI In keeping with the “plain language initiative” at NIH, the About NCBI section of the NCBI Web site presents many fundamentals of NCBI's bioinformatics tools and databases, including a science primer covering such topics as molecular genetics, genome mapping, Single Nucleotide Polymorphisms (SNPs) (Chapter 5), and microarray technology (Chapter 6). A model organism guide presents various model organisms and their uses in laboratory settings.As an introduction and orientation to NCBI's multifaceted Web site, the About NCBI section appeals to the general public, educators, and researchers alike.NCBI Site Map The NCBI Site Map serves as a guide to NCBI resources. It provides a comprehensive, linked list of resources, along with a brief description of each resource. An effective way to locate a resource of interest within the Site Map is to perform a Find in Page search, a function that is built into all commonly used Web browsers.Publications The NCBI News is a quarterly newsletter that includes articles on new services, new features,and basic research at NCBI, as well as how to use selected resources for common applications.The newsletter is available free of charge and is offered online and by print subscription.The User Services group also prepares fact sheets, brochures, and other public information materials to describe and illustrate NCBI services. A list of available materials is provided in the About NCBI section of the Web site, under News.The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookOverview articles entitled GenBank and Database Resources of the NCBI have also been published recently in the annual database issues of Nucleic Acids Research (1-3).Outreach NCBI's continuing emphasis on outreach to the scientific community is evident in its multifaceted program that includes exhibiting its services at scientific meetings, offering a variety of training courses, and developing Web-based tutorials and workshops.Exhibits at Scientific Meetings NCBI exhibits at approximately 15 scientific meetings per year, providing an opportunity for a wide range of researchers, students, and teachers to see demonstrations of NCBI resources and interact directly with NCBI staff. The current exhibit schedule is posted on the NCBI Web site in the About NCBI section, under NCBI at a Glance .Workshops are offered at select scientific meetings and include the standing workshops described below in the Training section, but workshops also can be customized for particular audiences. Meeting organizers who would like to invite NCBI to offer a workshop are encouraged to do so.Training Courses NCBI has a growing training program consisting of full-day, half-day, and two-hour courses that are usually a combination of lecture and computer-based formats. There are also advanced courses that are given over a more extended time period. Each is described briefly below, and further information on the training programs can be found in the Education section of the Web site, under NCBI Courses.A Field Guide to GenBank and Other NCBI Resources A Field Guide to GenBank and NCBI Molecular Biology Resources is a training course offered in a lecture format, followed by hands-on computer sessions. It is designed as a basic but broad introduction to NCBI tools and resources.Field Guide topics include the following: description and scope of the primary database,GenBank (Chapter 1); derivative databases, such as UniGene (Chapter 21), Entrez Gene (Chapter 19), and Reference Sequence (RefSeq) (Chapter 18); effective database searching using Entrez; NCBI structure databases and the structure viewer, Cn3D; sequence similarity searching using the BLAST programs; the Conserved Domain Database (CDD) and associatedsearch engine; and genome resources, including the NCBI assembly of the draft human genome, access to both finished and unfinished microbial genomes, and the genome Map Viewer.The course is offered by invitation at academic institutions as well as at selected scientific conferences. If you are interested in hosting a course at your institution or conference, write to info@, and your request will be routed to the course coordinator.The course is also offered four times a year at the NLM on the NIH campus in Bethesda,Maryland, and is free and open to anyone who would like to attend.More information on this course is available in the Education section of the NCBI Web site,under NCBI Courses . The Web site includes the course handout, slide presentations, and problem sets with answers. A schedule of planned courses at NLM and elsewhere is posted under Upcoming Courses .The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookMolecular Biology Information Resources This course is designed primarily for medical and science librarians or other professionals who are providing support services for molecular biology information resources. It provides an introduction to four categories of molecular biology information available from NCBI:nucleotide sequences, protein sequences, three-dimensional structures, and complete genomes and maps. An overview of search systems available at the NCBI, particularly Entrez and BLAST, emphasizes how search skills related to other types of information resources also apply to molecular biology databases. The course concludes with a discussion of various levels of molecular biology information services provided by librarians.The Medical Library Association approves this course for eight continuing education credit hours. The course has been given at 24 locations since May 1997. Because of the increase in NCBI services, courses are being revised and are not being scheduled at this time.More information on this course is available in the Education section of the NCBI Web site,under NCBI Courses . The Web site includes the course materials used for the lecture and a set of exercises.NCBI Advanced Workshop for Bioinformatics Information Specialists A new 5-day advanced course on NCBI resources has been developed as part of a collaborative project with a group of scientists and librarians who currently provide bioinformatics support services at their universities. The course provides detailed descriptive information as well as hands-on experience with handling a wide range of user questions. The course is designed for bioinformatics support staff based in university medical libraries so that they can, in turn, assist students, faculty, staff, and clinicians at their institutions in the use of molecular biology information resources. Additional information on this course is available in the Education section of the NCBI Web site.Specialized Mini-Courses The Service Desk staff also offers four mini-courses: BLAST QuickStart, Unmasking Genes in the Human Genome, Making Sense of DNA and Protein Sequences, and GenBank and PubMed Searching. Each is described briefly below. The purpose of the mini-courses is to focus on specific research application areas and address how to use multiple NCBI resources together to answer a research question. Additional problem-oriented mini-courses are under development.The courses are 2 hours each in length. An overview is given during the first hour in lectureformat, followed by a 1-hour hands-on session. Although primarily given on the NIH campus,NCBI is beginning to offer these workshops at outside institutions as well. Although the mini-courses were originally designed to be presented by an instructor, they are constructed in an online notebook format; therefore, it is possible to take the course on your own. Revisions to augment the online notebooks with lecture material and make the courses completely self-guided are currently under way.BLAST QuickStart!This mini-course is a practical introduction to the BLAST family of sequence-similarity search programs. Exercises range from simple searches to creative uses of the BLAST programs.Unmasking Genes in the Human GenomeThis mini-course covers how to find genes, promoters, and transcription factor-binding sites in human DNA sequences. It is designed around a program developed within User ServicesThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI Handbookcalled Greengene, which integrates the output of several gene-finding tools and allows a coding sequence and accompanying protein translation to be assembled from the exons detected by these programs. Because the output of several programs is integrated, there is increased reliability in exon selection.Making Sense of DNA and Protein Sequences In this course, participants find a gene within a eukaryotic DNA sequence. They then predict the function of the derived protein by seeking sequence similarities to proteins with documented function using BLAST and other tools. Finally, a 3D modeling template is located for the protein sequence using the Conserved Domain Search (CDD-Search).During the first hour, an instructor walks the class through an analysis of an uncharacterized Drosophila melanogaster genomic sequence from a GenBank record. During the second hour,participants perform the same analysis independently, using a different genomic sequence.GenBank and PubMed Searching This mini-course provides an overview of literature searching and sequence retrieval using the PubMed and Entrez database search interfaces. Exercises illustrate advanced search tips for using Entrez, many of which explore the use of the Preview/Index options for specifying parameters to limit the search results. The course also features 21 self-scoring exercises for GenBank.The NCBI Learning Center In addition to communication by email and phone provided through the Help Desk, a regular research consultation service provides one-on-one support for researchers in the NIH community. The consults are available by appointment and are provided in 1-hour time slots at the NIH Library as well as the NCBI training facility. Because of the success of the program,this type of service may be offered by appointment at selected scientific meetings in the future.CoreBio An innovative training program that began in 2001 aims to train molecular biologists for a new type of career as bioinformatics specialists who provide institutional support for users of computational biology tools. The NCBI Core Bioinformatics Facility (referred to as the CoreBio program) currently functions to train and support a network of bioinformatics specialists serving individual Institutes at NIH. NCBI's CoreBio facility trains Core members identified by their respective institutes in the use of its bioinformatics tools. The Core members,in turn, support the use of NCBI tools and databases by researchers at their institutes.The training is provided over a 9-week period, with students attending lectures and completing practical exercises in the morning and returning to their regular workplace in the afternoon.The coursework centers on one major topic each week and follows the rough schedule given below:WEEK 1: Introduction to the Sequence Databases WEEK 2: BLASTWEEK 3: The Human Genome WEEK 4: Genomic Biology WEEK 5: Molecular ModelingThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookWEEK 6: Web Page Development WEEK 7: Setting Up a BLAST Web Server WEEK 8: Interaction with Users WEEK 9: Practicum During week 9, the students pursue an institute-related project with the assistance of NCBI instructors. These projects run the gamut from the compilation of specialized datasets and data mining to the creation of novel BLAST interfaces and the construction of new data display tools. Students also develop a Web page to support the services they are developing for the respective Institutes at the NIH.Although currently a NIH-based program, other organizations are welcome to consider using the program as a model for development of similar initiatives to meet their bioinformatics support needs.Conclusion At NCBI, we encourage our users to contact us with questions, suggestions, and requests for training or presentations on NCBI services. We invite feedback on tutorials, FAQs, and other support materials and welcome suggestions regarding additional materials that would be useful in guiding users through the wide range of services offered by NCBI.References 1. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL. GenBank. Nucleic Acids Res 2002;30:17–20.99127 [PubMed: 11752243]2. Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM,Tatusova TA, Wagner L, Rapp BA. Database resources of the National Center for Biotechnology Information: 2002 update. Nucleic Acids Res 2002;30:13–16.99094 [PubMed: 11752242]3. Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM,Tatusova TA, Wagner L, Rapp BA. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2001;29:11–16.29800 [PubMed: 11125038]The NCBI Handbook The NCBI Handbook The NCBI Handbook The NCBI Handbook。

PubMed-中文使用手册

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Cn3D4.1使用指导说明中文版

Cn3D 4.1中文使用手册Yang Xin（yx3240106@）翻译生物软件网（）整理提供Welcome to the Cn3D 4.1 Tutorial! 目录•简介o Cn3D的基本功能o下载和安装Cn3Do文档约定o参考文献•寻找特定的结构(MMDB)o根据Entrez文献研究o根据Entrez 临近序列o通过BLAST搜索o通过已知的PDB标识•在Cn3D中察看特定的序列结构o Cn3D的基本控制操作结构窗体的主菜单样式面板o Cn3D的序列阅读器•结构比较(VAST)o在Cn3D中察看结构比较结果Cn3D的比对察看器Cn3D的比对模块•导入和保存o导入序列和空间结构o可见的序列保守性•注释结构o骨架和界标o自定义样式•保存空间结构和图像o将Cn3D用于交互式图形•高级设置o动画控制o显示无序晶体o类型搜寻o导入用户PDB文件•比对编辑o使用编辑器o校正队列错误o将序列合并到多重序列中简介这是 Cn3D 4.1的使用手册。

希望能够向初次使用或是曾经使用过Cn3D的用户提供一个关于本软件的基本特点的指导。

新用户可能希望通过阅读这篇文档来学习如何使用Cn3D,而有经验的用户则可以通过上面的目录和超连接直接跳转到自己感兴趣的章节。

本手册并不是对程序功能的详尽的介绍。

在Cn3D的安装程序里包含有关于Cn3D的用户界面和详细功能介绍的帮助文档。

—见Cn3D_Commands.chm。

Cn3D 的基本功能Cn3D 是一个生物分子的三维结构、序列以及序列比对结果的可视化工具。

Cn3D可以通过基于结构的序列比较来显示生物分子结构之间的比较，从而了解相关蛋白的那一个结构域在结构与序列上表现得更为保守。

同时，可以自定义标签的特性，高品质的OpenGL 的画质，还有多样的文件输出格式，都使得Cn3D成为文献注释的强大工具。

新版Pubmed最全实用教程（超全收藏版）

新版Pubmed最全实用教程（超全收藏版）PubMed 是一个免费的搜寻引擎，提供生物医学方面的论文搜寻以及摘要。

它的数据库来源为MEDLINE。

其核心主题为医学，但亦包括其他与医学相关的领域，像是护理学或者其他健康学科。

它同时也提供对于相关生物医学资讯上相当全面的支援，像是生化学与细胞生物学。

该搜寻引擎是由美国国立医学图书馆提供，作为 Entrez 资讯检索系统的一部分。

PubMed 的资讯并不包括期刊论文的全文，但可能提供指向全文提供者(付费或免费)的链接。

PubMed是因特网上使用最广泛的免费MEDLINE,是美国国家医学图书馆(NLM)所属的国家生物技术信息中心(NCBI)于2000年4月开发的,基于WEB的生物医学信息检索系统,它是NCBI Entrez整个数据库查询系统中的一个。

PubMed界面提供与综合分子生物学数据库的链接，其内容包括:DNA与蛋白质序列，基因图数据，3D蛋白构象，人类孟德尔遗传在线，也包含着与提供期刊全文的出版商网址的链接等。

PubMed系统的特征工具栏提供辅助检索功能、侧栏提供其它检索如期刊数据库检索、主题词数据库检索和特征文献检索。

提供原文获取服务免费提供题录和文摘，可与提供原文的网址链接，提供检索词自动转换匹配，操作简便、快捷。

Pubmed最近也是改头换面了，为了能够帮助大家快速熟悉上手新版Pubmed，我们这里进行了常用功能的总结，供大家参考。

首页是这样的：目录•基本检索•高级检索•Mesh主题词检索•常用检索技巧•如何让Pubmed自动发送最新文献•如何使用Pubmed直接复制黏贴参考文献基本检索基本检索是PubMed最常用的检索方式。

在PubMed基本检索框中输入检索词，点击Search即可检索文献。

比如在检索框中直接输入septic shock，点击检索。

结果显示界面如下，中间主体内容为检索获得的文献，左侧主体内容为Pubmed自带或者你自己自主设置的过滤器。

美国国家生物信息中心使用介绍

NCBI (National Center for Biotechnology Information), 美国国家生物技术信息中心[url]/[/url]NCBI是NIH的国立医学图书馆（NLM）的一个分支。

NCBI提供检索的服务包括：1．GenBank（NIH遗传序列数据库）：一个可以公开获得所有的DNA序列的注释过的收集。

GenBank是由NCBI受过分子生物学高级训练的工作人员通过来自各个实验室递交的序列和同国际核酸序列数据库（EMBL和DDBJ）交换数据建立起数据库的。

它同日本和欧洲分子生物学实验室的DNA数据库共同构成了国际核酸序列数据库合作。

这三个组织每天交换数据。

其中的数据以指数形式增长，最近的数据为它已经有来自47000个物种的30亿个碱基。

2．Molecular Databases（分子数据库）：Nucleotide Sequence（核酸序列库）：从NCBI其他如Genbank数据库中收集整理核酸序列，提供直接的检索。

Protein Sequence （蛋白质序列库）：与核酸类似，也是从NCBI多个不同资源中编译整理的，方便研究者的直接查询。

Structure（结构）-——关于NCBI结构小组的一般信息和他们的研究计划，另外也可以访问三维蛋白质结构的分子模型数据库（MMDB）和用来搜索和显示结构的相关工具。

MMDB：分子模型数据库—一个关于三维生物分子结构的数据库，结构来自于X-ray晶体衍射和NMR色谱分析。

Taxonomy（分类学）——NCBI的分类数据库，包括大于7万余个物种的名字和种系，这些物种都至少在遗传数据库中有一条核酸或蛋白序列。

其目的是为序列数据库建立一个一致的种系发生分类学。

3．Literature Databases（文献数据库）（1）PubMed是NLM提供的一项服务，能够对MEDLINE上超过1200万条的上世纪六十年代中期至今的杂志引用和其他的生命科学期刊进行访问，并可以连接到参与的出版商网络站点的全文文章和其他相关资源。

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它提供的视频教程⾮常丰富并且质量很⾼，包括：PS 教程、⼿机摄影教程、Ai 做图教程、Excel 教程、Word 教程、PPT 教程、Pr 视频剪辑教程、Ae 视频特效教程、Au ⾳频教程教程、Flash 教程、做⽹页教程、css 样式教程、js 教程、Cad 制图教程、电路制作教程、模电教程、Windows 教程、⾊彩搭配教程、Prezi 演⽰教程、Keynote 教程、做图标教程、玩字体教程。

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pubmed使用手册1

The NCBI Handbookdata daily so that all three databases should contain the same set of sequences. Members of the DDBJ, EMBL, and GenBank staff meet annually to discuss technical issues, and an international advisory board meets with the database staff to provide additional guidance. An entry can only be updated by the database that initially prepared it to avoid conflicting data at the three sites.The Collaboration created a Feature Table Definition that outlines legal features and syntax for the DDBJ, EMBL, and GenBank feature tables. The purpose of this document is to standardize annotation across the databases. The presentation and format of the data are different in the three databases, however, the underlying biological information is the same.Confidentiality of Data When scientists submit data to GenBank, they have the opportunity to keep their data confidential for a specified period of time. This helps to allay concerns that the availability of their data in GenBank before publication may compromise their work. When the article containing the citation of the sequence or its Accession number is published, the sequence record is released. The database staff request that submitters notify GenBank of the date of publication so that the sequence can be released without delay. The request to release should be sent to gb-admin@.Direct Submissions The typical GenBank submission consists of a single, contiguous stretch of DNA or RNA sequence with annotations. The annotations are meant to provide an adequate representation of the biological information in the record. The GenBank Feature Table Definition describes the various features and subsequent qualifiers agreed upon by the International Nucleotide Sequence Database Collaboration.Currently, only nucleotide sequences are accepted for direct submission to GenBank. These include mRNA sequences with coding regions, fragments of genomic DNA with a single gene or multiple genes, and ribosomal RNA gene clusters. If part of the nucleotide sequence encodes a protein, a conceptual translation, called a CDS (coding sequence), is annotated. The span of the CDS feature is mapped to the nucleotide sequence encoding the protein. A protein Accession number (/protein_id) is assigned to the translation product, which will subsequently be added to the protein databases.Multiple sequences can be submitted together. Such batch submissions of non-relatedsequences may be processed together but will be displayed in Entrez (Chapter 15) as single records. Alternatively, by using the Sequin submission tool (Chapter 12), a submitter can specify that several sequences are biologically related. Such sequences are classified as environmental sample sets, population sets, phylogenetic sets, mutation sets, or segmented sets. Each sequence within a set is assigned its own Accession number and can be viewed independently in Entrez. However, with the exception of segmented sets, each set is also indexed within the PopSet division of Entrez, thus allowing scientists to view the relationship between the sequences.What defines a set? Environmental sample, population, phylogenetic, and mutation sets all contain a group of sequences that spans the same gene or region of the genome. Environmental samples are derived from a group of unclassified or unknown organisms. A population set contains sequences from different isolates of the same organism. A phylogenetic set contains sequences from different organisms that are used to determine the phylogenetic relationship between them. Sequencing multiple mutations within a single gene gives rise to a mutation set.The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookAll sets, except segmented sets, may contain an alignment of the sequences within them and might include external sequences already present in the database. In fact, the submitter can begin with an existing alignment to create a submission to the database using the Sequin submission tool. Currently, Sequin accepts FASTA+GAP, PHYLIP, MACAW, NEXUS Interleaved, and NEXUS Contiguous alignments. Submitted alignments will be displayed in the PopSet section of Entrez.Segmented sets are a collection of noncontiguous sequences that cover a specified genetic region. The most common example is a set of genomic sequences containing exons from a single gene where part or all of the intervening regions have not been sequenced. Each member record within the set contains the appropriate annotation, exon features in this case. However,the mRNA and CDS will be annotated as joined features across the individual records.Segmented sets themselves can be part of an environmental sample, population, phylogenetic,or mutation set.Bulk Submissions: High-Throughput Genomic Sequence (HTGS)HTGS entries are submitted in bulk by genome centers, processed by an automated system,and then released to GenBank. Currently, about 30 genome centers are submitting data for a number of organisms, including human, mouse, rat, rice, and Plasmodium falciparum , the malaria parasite.HTGS data are submitted in four phases of completion: 0, 1, 2, and 3. Phase 0 sequences are one-to-few reads of a single clone and are not usually assembled into contigs. They are low-quality sequences that are often used to check whether another center is already sequencing a particular clone. Phase 1 entries are assembled into contigs that are separated by sequence gaps,the relative order and orientation of which are not known (Figure 1). Phase 2 entries are also unfinished sequences that may or may not contain sequence gaps. If there are gaps, then the contigs are in the correct order and orientation. Phase 3 sequences are of finished quality and have no gaps. For each organism, the group overseeing the sequencing effort determines the definition of finished quality.The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookDiagram showing the orientation and gaps that might be expected in high-throughput sequence from phases 1, 2, and 3.Phase 0, 1, and 2 records are in the HTG division of GenBank, whereas phase 3 entries go into the taxonomic division of the organism, for example, PRI (primate) for human. An entry keeps its Accession number as it progresses from one phase to another but receives a new Accession.Version number and a new gi number each time there is a sequence change.Submitting Data to the HTG DivisionTo submit sequences in bulk to the HTG processing system, a center or group must set up an FTP account by writing to htgs-admin@. Submitters frequently use two tools to create HTG submissions, Sequin or fa2htgs. Both of these tools require FASTA-formatted sequence, i.e., a definition line beginning with a “greater than” sign (“>”) followed by a unique identifier for the sequence. The raw sequence appears on the lines after the definition line. For sequences composed of contigs separated by gaps, a modified FASTA format is used. In addition, Sequin users must modify the Sequin configuration file so that the HTG genome center features are enabled.fa2htgs is a command-line program that is downloaded to the user's computer. The submitter invokes a script with a series of parameters (arguments) to create a submission. It has an advantage over Sequin in that it can be set up by the user to create submissions in bulk from multiple files.Submissions to HTG must contain three identifiers that are used to track each HTG record: the genome center tag, the sequence name, and the Accession number. The genome center tag is assigned by NCBI and is generally the FTP account login name. The sequence name is a unique identifier that is assigned by the submitter to a particular clone or entry and must be unique within the group's submissions. When a sequence is first submitted, it has only a sequence name and genome center tag; the Accession number is assigned during processing. All updates to that entry must include the center tag, sequence name, and Accession number, or processing will fail.The HTG Processing PathwaySubmitters deposit HTGS sequences in the form of Seq-submit files generated by Sequin,fa2htgs, or their own ASN.1 dumper tool into the SEQSUBMIT directory of their FTP account.Every morning, scripts automatically pick up the files from the FTP site and copy them to the processing pathway, as well as to an archive. Once processing is complete and if there are no errors in the submission, the files are automatically loaded into GenBank. The processing time is related to the number of submissions that day; therefore, processing can take from one to many hours.Entries can fail HTG processing because of three types of problems:1Formatting: submissions are not in the proper Seq-submit format.The NCBI HandbookThe NCBI Handbook The NCBI Handbook The NCBI Handbook2Identification: submissions may be missing the genome center tag, sequence name,or Accession number, or this information is incorrect.3Data: submissions have problems with the data and therefore fail the validator checks.When submissions fail HTG processing, a GenBank annotator sends email to the sequencing center, describing the problem and asking the center to submit a corrected entry. Annotators do not fix incorrect submissions; this ensures that the staff of the submitting genome center fixes the problems in their database as well.The processing pathway also generates reports. For successful submissions, two files are generated: one contains the submission in GenBank flat file format (without the sequence);and another is a status report file. The status report file, ac4htgs, contains the genome center,sequence name, Accession number, phase, create date, and update date for the submission.Submissions that fail processing receive an error file with a short description of the error(s)that prevented processing. The GenBank annotator also sends email to the submitter, explaining the errors in further detail.Additional Quality Assurance When successful submissions are loaded into GenBank, they undergo additional validation checks. If GenBank annotators find errors, they write to the submitters, asking them to fix these errors and submit an update.Whole Genome Shotgun Sequences (WGS)Genome centers are taking multiple approaches to sequencing complete genomes from a number of organisms. In addition to the traditional clone-based sequencing whose data are being submitted to HTGS, these centers are also using a WGS approach to sequence the genome. The shotgun sequencing reads are assembled into contigs, which are now being accepted for inclusion in GenBank. WGS contig assemblies may be updated as the sequencing project progresses and new assemblies are computed. WGS sequence records may also contain annotation, similar to other GenBank records.Each sequencing project is assigned a stable project ID, which is made up of four letters. The Accession number for a WGS sequence contains the project ID, a two-digit version number,and six digits for the contig ID. For instance, a project would be assigned an Accession number AAAX00000000. The first assembly version would be AAAX01000000. The last six digits of this ID identify individual contigs. A master record for each assembly is created. This master record contains information that is common among all records of the sequencing project, suchas the biological source, submitter, and publication information. There is also a link to the range of Accession numbers for the individual contigs in this assembly.WGS submissions can be created using tbl12asn, a utility that is packaged with the Sequin submission software. Information on submitting these sequences can be found at Whole Genome Shotgun Submissions.Bulk Submissions: EST, STS, and GSSExpressed Sequence Tags (EST), Sequence Tagged Sites (STSs), and Genome SurveySequences (GSSs) sequences are generally submitted in a batch and are usually part of a large sequencing project devoted to a particular genome. These entries have a streamlined submission process and undergo minimal processing before being loaded to GenBank.ESTs are generally short (<1 kb), single-pass cDNA sequences from a particular tissue and/or developmental stage. However, they can also be longer sequences that are obtained byThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI Handbookdifferential display or Rapid Amplification of cDNA Ends (RACE) experiments. The common feature of all ESTs is that little is known about them; therefore, they lack feature annotation.STSs are short genomic landmark sequences (1). They are operationally unique in that they are specifically amplified from the genome by PCR amplification. In addition, they define a specific location on the genome and are, therefore, useful for mapping.GSSs are also short sequences but are derived from genomic DNA, about which little is known.They include, but are not limited to, single-pass GSSs, BAC ends, exon-trapped genomic sequences, and Alu PCR sequences.EST, STS, and GSS sequences reside in their respective divisions within GenBank, rather than in the taxonomic division of the organism. The sequences are maintained within GenBank in the dbEST, dbSTS, and dbGSS databases.Submitting Data to dbEST, dbSTS, or dbGSS Because of the large numbers of sequences that are submitted at once, dbEST, dbSTS, and dbGSS entries are stored in relational databases where information that is common to all sequences can be shared. Submissions consist of several files containing the common information, plus a file of the sequences themselves. The three types of submissions have different requirements, but all include a Publication file and a Contact file. See the dbEST,dbSTS, and dbGSS pages for the specific requirements for each type of submission.In general, users generate the appropriate files for the submission type and then email the files to batch-sub@. If the files are too big for email, they can be deposited into a FTP account. Upon receipt, the files are examined by a GenBank annotator, who fixes any errors when possible or contacts the submitter to request corrected files. Once the files are satisfactory, they are loaded into the appropriate database and assigned Accession numbers.Additional formatting errors may be detected at this step by the data-loading software, such as double quotes anywhere in the file or invalid characters in the sequences. Again, if the annotator cannot fix the errors, a request for a corrected submission is sent to the user. After all problems are resolved, the entries are loaded into GenBank.Bulk Submissions: HTC and FLIC HTC records are High-Throughput cDNA/mRNA submissions that are similar to ESTs but often contain more information. For example, HTC entries often have a systematic gene name (not necessarily an official gene name) that is related to the lab or center that submitted them,and the longest open reading frame is often annotated as a coding region.FLIC records, Full-Length Insert cDNA, contain the entire sequence of a cloned cDNA/mRNA.Therefore, FLICs are generally longer, and sometimes even full-length, mRNAs. They are usually annotated with genes and coding regions, although these may be lab systematic names rather than functional names.HTC SubmissionsHTC entries are usually generated with Sequin or tbl2asn, and the files are emailed to gb-sub@. If the files are too big for email, then by prior arrangement, thesubmitter can deposit the files by FTP and send a notification to gb-admin@ that files are on the FTP site.The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookHTC entries undergo the same validation and processing as non-bulk submissions. Once processing is complete, the records are loaded into GenBank and are available in Entrez and other retrieval systems.FLIC Submissions FLICs are processed via an automated FLIC processing system that is based on the HTG automated processing system. Submitters use the program tbl2asn to generate their submissions. As with HTG submissions, submissions to the automated FLIC processing system must contain three identifiers: the genome center tag, the sequence name (SeqId), and the Accession number. The genome center tag is assigned by NCBI and is generally the FTP account login name. The sequence name is a unique identifier that is assigned by the submitter to a particular clone or entry and must be unique within the group's FLIC submissions. When a sequence is first submitted, it has only a sequence name and genome center tag; the Accession number is assigned during processing. All updates to that entry include the center tag, sequence name, and Accession number, or processing will fail.The FLIC Processing Pathway The FLIC processing system is analogous to the HTG processing system. Submitters deposit their submissions in the FLICSEQSUBMIT directory of their FTP account and notify us that the submissions are there. We then run the scripts to pick up the files from the FTP site and copy them to the processing pathway, as well as to an archive. Once processing is complete and if there are no errors in the submission, the files are automatically loaded into GenBank.As with HTG submissions, FLIC entries can fail for three reasons: problems with the format,problems with the identification of the record (the genome center, the SeqId, or the Accession number), or problems with the data itself. When submissions fail FLIC processing, a GenBank annotator sends email to the sequencing center, describing the problem and asking the center to submit a corrected entry. Annotators do not fix incorrect submissions; this ensures that the staff of the submitting genome center fixes the problems in their database as well. At the completion of processing, reports are generated and deposited in the submitter's FTP account,as described for HTG submissions.Submission Tools Direct submissions to GenBank are prepared using one of two submission tools, BankIt or Sequin.BankItBankIt is a Web-based form that is a convenient and easy way to submit a small number of sequences with minimal annotation to GenBank. To complete the form, a user is prompted to enter submitter information, the nucleotide sequence, biological source information, and features and annotation pertinent to the submission. BankIt has extensive Help documentation to guide the submitter. Included with the Help document is a set of annotation examples that detail the types of information that are required for each type of submission. After theinformation is entered into the form, BankIt transforms this information into a GenBank flatfile for review. In addition, a number of quality assurance and validation checks ensure that the sequence submitted to GenBank is of the highest quality. The submitter is asked to include spans (sequence coordinates) for the coding regions and other features and to include amino acid sequence for the proteins that derive from these coding regions. The BankIt validator compares the amino acid sequence provided by the submitter with the conceptual translation of the coding region based on the provided spans. If there is a discrepancy, the submitter is requested to fix the problem, and the process is halted until the error is resolved. To preventThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI Handbookthe deposit of sequences that contain cloning vector sequence, a BLAST similarity search is performed on the sequence, comparing it to the VecScreen database. If there is a match to this database, the user is asked to remove the contaminating vector sequence from their submission or provide an explanation as to why the screen was positive. Completed forms are saved in ASN.1 format, and the entry is submitted to the GenBank processing queue. The submitter receives confirmation by email, indicating that the submission process was successful.Sequin Sequin is more appropriate for complicated submissions containing a significant amount of annotation or many sequences. It is a stand-alone application available on NCBI's FTP site.Sequin creates submissions from nucleotide and amino acid sequences in FASTA format with tagged biological source information in the FASTA definition line. As in BankIt, Sequin has the ability to predict the spans of coding regions. Alternatively, a submitter can specify the spans of their coding regions in a five-column, tab-delimited table and import that table into Sequin. For submitting multiple, related sequences, e.g., those in a phylogenetic or population study, Sequin accepts the output of many popular multiple sequence-alignment packages,including FASTA+GAP, PHYLIP, MACAW, NEXUS Interleaved, and NEXUS Contiguous.It also allows users to annotate features in a single record or a set of records globally. For more information on Sequin, see Chapter pleted Sequin submissions should be emailed to GenBank at gb-sub@rger files may be submitted by SequinMacrosend.Sequence Data Flow and Processing: From Laboratory to GenBank Triage All direct submissions to GenBank, created either by Sequin or BankIt, are processed by the GenBank annotation staff. The first step in processing submissions is called triage. Within 48hours of receipt, the database staff reviews the submission to determine whether it meets the minimal criteria for incorporation into GenBank and then assigns an Accession number to each sequence. All sequences must be >50 bp in length and be sequenced by, or on behalf of, the group submitting the sequence. GenBank will not accept sequences constructed in silico ;noncontiguous sequences containing internal, unsequenced spacers; or sequences for which there is not a physical counterpart, such as those derived from a mix of genomic DNA and mRNA. Submissions are also checked to determine whether they are new sequences or updates to sequences submitted previously. After receiving Accession numbers, the sequences are put into a queue for more extensive processing and review by the annotation staff.IndexingTriaged submissions are subjected to a thorough examination, referred to as the indexing phase.Here, entries are checked for:1Biological validity. For example, does the conceptual translation of a coding regionmatch the amino acid sequence provided by the submitter? Annotators also ensure that the source organism name and lineage are present, and that they are represented in NCBI's taxonomy database. If either of these is not true, the submitter is asked to correct the problem. Entries are also subjected to a series of BLAST similaritysearches to compare the annotation with existing sequences in GenBank.2Vector contamination. Entries are screened against NCBI's UniVec database to detect contaminating cloning vector.The NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI Handbook3Publication status. If there is a published citation, PubMed and MEDLINE identifiers are added to the entry so that the sequence and publication records can be linked in Entrez.4Formatting and spelling. If there are problems with the sequence or annotation, the annotator works with the submitter to correct pleted entries are sent to the submitter for a final review before release into the public database. If the submitters requested that their sequences be released after processing, they have 5 days to make changes prior to release. The submitter may also request that GenBank hold their sequence until a future date. The sequence must become publicly available once the Accession number or the sequence has been published. The GenBank annotation staff currently processes about 1,900 submissions per month, corresponding to approximately 20,000sequences.GenBank annotation staff must also respond to email inquiries that arrive at the rate of approximately 200 per day. These exchanges address a range of topics including:•updates to existing GenBank records, such as new annotation or sequence changes •problem resolution during the indexing phase •requests for release of the submitter's sequence data or an extension of the hold date •requests for release of sequences that have been published but are not yet available in GenBank •lists of Accession numbers that are due to appear in upcoming issues of a publisher's journals •reports of potential annotation problems with entries in the public database •requests for information on how to submit data to GenBank One annotator is responsible for handling all email received in a 24-hour period, and all messages must be acted upon and replied to in a timely fashion. Replies to previous emails are forwarded to the appropriate annotator.Processing Tools The annotation staff uses a variety of tools to process and update sequence submissions.Sequence records are edited with Sequin, which allows staff to annotate large sets of records by global editing rather than changing each record individually. This is truly a time saver because more than 100 entries can be edited in a single step (see Chapter 12 on Sequin formore details). Records are stored in a database that is accessed through a queue management tool that automates some of the processing steps, such as looking up taxonomy and PubMed data, starting BLAST jobs, and running automatic validation checks. Hence, when an annotator is ready to start working on an entry, all of this information is ready to view. In addition, all of the correspondence between GenBank staff and the submitter is stored with the entry. For updates to entries already present in the public database, the live version of the entry is retrieved from ID, and after making changes, the annotator loads the entry back into the public database.This entry is available to the public immediately after loading.Microbial GenomesThe GenBank direct submissions group has processed more than 50 complete microbialgenomes since 1996. These genomes are relatively small in size compared with their eukaryotic counterparts, ranging from five hundred thousand to five million bases. Nonetheless, these genomes can contain thousands of genes, coding regions, and structural RNAs; therefore,processing and presenting them correctly is a challenge. Currently, the DDBJ/EMBL/GenBankThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookNucleotide Sequence Database Collaboration has a 350-kilobase (kb) upper size limit for sequence entries. Because a complete bacterial genome is larger than this arbitrary limit, it must be split into pieces. GenBank routinely splits complete microbial genomes into 10-kb pieces with a 60-bp overlap between pieces. Each piece contains approximately 10 genes. A CON entry, containing instructions on how to put the pieces back together, is also made. The CON entry contains descriptor information, such as source organism and references, as well as a join statement providing explicit instructions on how to generate the complete genome from the pieces. The Accession number assigned to the CON record is also added as a secondary Accession number on each of the pieces that make up the complete genome (see Figure 2).Page 10The NCBI Handbook The NCBI Handbook The NCBI Handbook The NCBI HandbookA GenBank CON entry for a complete bacterial genome The information toward the bottom of the record describes how to generate the complete genome from the pieces.Submitting and Processing Data Submitters of complete genomes are encouraged to contact us at genomes@before preparing their entries. A FTP account is required to submit large files, and the submission should be deposited at least 1 month before publication to allow for processing time and coordinated release before publication. In addition, submitters are required to follow certain guidelines, such as providing unique identifiers for proteins and systematic names for all genes. Entries should be prepared with the submission tool tbl2asn, a utility that is part of the Sequin package (Chapter 12). This utility creates an ASN.1 submission file from a five-column, tab-delimited file containing feature annotation, a FASTA-formatted nucleotide sequence, and an optional FASTA-formatted protein sequence.Complete genome submissions are reviewed by a member of the GenBank annotation staff to ensure that the annotation and gene and protein identifiers are correct, and that the entry is in proper GenBank format. Any problems with the entry are resolved through communication with the submitter. Once the record is complete, the genome is carefully split into its component pieces. The genome is split so that none of the breaks occurs within a gene or coding region.A member of the annotation staff performs quality assurance checks on the set of genomeThe NCBI HandbookThe NCBI HandbookThe NCBI HandbookThe NCBI Handbook。

PubMed中文使用手册 (PDF)

PubMed中文使用手册Jeffrey Wu（一）PubMed简介：PubMed是美国家医学图书馆(NLM)下属的国家生物技术信息中心(NCBI)开发的、基于WWW的查询系统。

PubMed是NCBI Entrez 数个数据库查询系统下中的一个。

PubMed 是提供免费的MEDLINE、PREMEDLINE与其他相关数据库接入服务，MEDLINE是一个拥有1亿字条的巨大数据库。

PubMed也包含着与提供期刊全文的出版商网址的链接，来自第三方的生物学数据，序列中心的数据等等。

PubMed提供与综合分子生物学数据库的链接与接入服务，这个数据库归NCBI所有，其内容包括：DNA与蛋白质序列，基因图数据、3D蛋白构象，人类孟德尔遗传在线。

（二）页面介绍:（更新很快，但其内容变化一般不大）在你的浏览器中的URL地址框中健入/pubmed/并单击回车键后，你将进入Pubmed的主页面。

如图：1. 主页面左侧框的介绍（注：Cubby和tutorial为最新加入的）MeSh Browser你可以用它来分层浏览MesH表Single Citation Matcher通过填表的形式输入期刊的信息可以找到某单篇的文献或整个期刊的内容。

Batch Citation Matcher用一种特定的形式输入期刊的信息一次搜索多篇文献。

Clinical Queries这一部分为临床医生设置，通过过滤的方式将搜索的文献固定在4个范围：治疗、诊断、病原学与预后。

Old PubMed (使用以前的PubMed查询方式)关于每一项的具体使用方法, 后面将会有详细介绍。

Related ResourcesOrder Documents提供一种收费性质服务，可以使用户在当地得到文献的全文拷贝（费用与发送方式各不相同）。

Grateful Med是对另一个NLM基于网络的查询系统的链接。

Grateful Med也提供MEDLINE的接入，并且还有一些其他的数据库如AIDSLINE、HISTLINE等等。

EndNote入门教程

EndNote入门教程信息组第一部分 EndNote的安装 (2)一、下载解压 (2)二、EndNote的安装 (2)三、升级到EndNote9.0.1 (2)第二部分 EndNote的使用 (3)一、创建EndNote文献数据库 (3)二、新建Reference (3)三、联机获取文献条目 (4)1、选择联机数据库 (4)2、从网站导入数据 (7)四、打开EndNote文献数据库 (9)五、EndNote reference library窗口 (9)六、预览参考文献 (10)七、参考文献排序 (11)八、在 Microsoft Word 中使用 EndNote 撰写文章 (11)1、撰写文章 (11)2、在文章中插入参考文献 (11)3、按要求输出参考文献的格式 (13)4、保存文章 (15)5、移除EndNote控制代码 (15)第三部分 EndNote的其他教程 (16)一、EndNote中文使用手册 (16)二、EndNote实用基础 (17)三、视频教程 (17)第一部分 EndNote的安装一、下载解压从论坛下载压缩包(大概81M)，然后右键单击文件图标，选择“解压到EndNote v9.0 Final”。

如图1.1图1.1二、EndNote的安装打开解压的EndNote v9.0 Fina文件夹，双击安装文件“SETUP.EXE”（如图1.2），一直点击“Next”按钮，最后点击“Finish”完成安装。

图1.2三、升级到EndNote9.0.1为了更好地支持中文，要对安装的9.0升级到9.0.1版本，双击EndNote v9.0 Final文件夹中的“EN901Patch.msp”图标（如图1.3），一直点击“Next”按钮，最后点击“Finish”完成升级。

图1.3第二部分 EndNote的使用一、创建EndNote文献数据库打开EndNote Program后，会跳出一个窗口（如图2.1），选择Create a new EndNote library，创建一个空白的文献数据库。

NCBI资源介绍及使用手册

NCBI资源介绍及使用手册NCBI资源介绍及使用手册1、概述1.1 NCBI简介1.2 NCBI的作用和意义2、NCBI数据库2.1 PubMed2.1.1 检索和浏览文献2.1.2 发表论文的要求和流程2.2 GenBank2.2.1 遗传序列数据的获取和使用2.2.2 序列比对和分析工具的使用2.3 Protein Data Bank（PDB）2.3.1 蛋白质结构数据的检索和浏览 2.3.2 分析蛋白质结构的工具和方法 2.4 Gene Expression Omnibus（GEO）2.4.1 基因表达数据的获取和分析2.4.2 基因表达谱的解读和应用2.5 NCBI BLAST2.5.1 序列比对的基本原理和步骤2.5.2 使用BLAST进行序列比对和注释3、NCBI工具与资源3.1 Primer-BLAST3.1.1 引物设计的基本原理3.1.2 使用Primer-BLAST进行引物设计 3.2 BLAST+3.2.1 BLAST+的功能和特点3.2.2 BLAST+的安装和使用方法3.3 Entrez3.3.1 Entrez数据库的分类和查询方法 3.3.2 使用Entrez进行数据获取和处理 3.4 NCBI Genome Workbench3.4.1 基因组数据的可视化和分析3.4.2 使用Genome Workbench进行基因组研究4、高级应用4.1 NCBI数据挖掘与分析4.1.1 通过NCBI进行序列数据挖掘4.1.2 利用NCBI进行基因组学研究4.2 NCBI数据整合与综合分析4.2.1 结合多个NCBI数据库进行综合分析4.2.2 多种数据源的整合与分析5、附件附件1、NCBI常用工具附件2、实例数据集注释：1、PubMed: 一个由美国国家医学图书馆维护的生物医学文献库，包括了大量的生物医学文献摘要和全文。

2、GenBank: 一个由美国国家生物技术信息中心维护的遗传序列数据库，包含了已知生物学序列的大部分信息。

pubmed文献检索系统使用指南

PubMed医学文献检索系统PubMed是因特网上重要的免费文献检索系统。

目前全球最著名的医学文献数据库系统是美国国立医学图书馆的MEDLINE，该数据库重数据免费提供给各个检索系统的开发商，因此在因特网上有重多的免费MEDLINE检索系统。

这些系统所涵盖的文献年代、检索结果的输出格式以及检索途径各不相同，但是，目前被医务人员广泛使用的仍然是美国国立医学图书馆的PubMed系统PubMed和NCBI：1．美国国立医学图书馆“NLM”2．早在1879年，编译医学文献的检索刊物IM3．1964年采用计算机进行电子编辑和排版，在此基础上开发了“医学文献分析与检索系统”（即著名的MEDLARS）4．1971年正式建立了钙系统的联机系统，称为“MEDLARS联机检索系统，MEDLARS online,既MEDLINE 系统。

5．PubMed则是NLM的国家生物信息中心（National Center for Biotechnology Information, NCBI）开发的一个以网络为基础的检索系统，自1997年免费提供服务PubMed ――特点：PubMed具有MEDLINE 所具有的各种检索和数据库优势，同时还具有以下特点：⏹连接广泛：包括对外链接和对内链接，对内指与NCBI其它数据库的链接和PubMed文献相似度计算后的相关文献链接，对外连接指出版商提供的文献全文的连接，有免费和需要注册的。

⏹更新速度快：出版商直接把电子版提供给NLM⏹收录文献范围广：三个层次的数据库：MEDLINE数据库、PreMEDLINE数据库和出版商直接提供的文献数据库等PubMed ――收录范围总体包括：⏹收录年限：1966～⏹收录内容：70多个国家和地区的4000余种生物医学期刊的文献和一些非医学内容的文献，主要是MEDLINE。

内容涉及医学、护理、牙科、兽医、健康保健系统、前临床医学等学科，另外有非医学内容的文献，如science 和nature中具有地理学方面的文献。

文献检索

• 专著（monograph)
针对某一专门题目分章节做出系统深入全面叙述的一种著作
• 参考工具书（Reference books)
根据一定需要收集有关资料并按特定的方法编排起来供人查考的文献
参考ห้องสมุดไป่ตู้具书
• • • • • • 字典、词典（dictionary) 百科全书（encyclopedia) 年鉴（yearbook, manual, almanac) 手册（handbook) 指南（directory) 药学工具书：药典—Martindale: Extra pharmacopiea, 手册—Merck Index, 字典—中药大辞典
• 核心期刊研究中文核心期刊要目总览 http://202.38.232.84/evaluation/ 中国科学引文数据库（CSCD）中国科技论文引文数据库（CSTPC） / 中国社会科学引文数据库（CSSCI） • 期刊评价影响因子（IF）、主办单位、学会背景、检索工具收录
专利文献(patent document)
• 指专利局公布或归档的与专利有关的文献，包括专利说明书、专利公报、专利分类资料、专利检索工具以及专利从申请到结束的全过程中包括的一些文件和资料 • 专利说明书是专利发明人或申请人为获得某项发明的专利权向国家专利主管部门递交的有关该发明创造的详细技术说明书，它说明该项发明的目的、用途、特点、效果、详述工艺过程、技术细节，并附图表和各种数据
• 半衰期： 18世纪为80～90年 19～20世纪初30年 20世纪60年代15年 20世纪80年代5年 21世纪初3年左右
文献数量
• 全世界每天发表的论文达13000～14000 篇，每年登记的新专利达70万项，每年出版的图书达50多万种。 Pubmed文献： 1980年 28万 1990年 40万 2000年 53万 2010年 93万

功能磁共振数据分析手册-第1章-翻译版

第1章引言翻译：yingers, nancyxyz, 灵犀校对：Amygdala本书的目的是为读者介绍功能磁共振(fMRI)数据处理和分析的方法及基本原理。

1.1 fMRI简介从20世纪90年代开始，fMRI的发展引起了科学界的轰动。

图1.1所显示的是PubMed数据库中与这一技术相关的生物医学文献数量，从数据增长情况我们可以明显地看到fMRI的发展趋势。

在1996年，仅用一周的时间就可以阅读完所有的fMRI文献；但现在，甚至连前一周发表的文献都读不完。

fMRI技术之所以可以如此快速地发展，得益于它可以比PET更安全而无创伤的获取脑活动成像，并且具有更高的空间和相对较高的时间分辨率。

图1.1. 1992年以来，每年PubMed数据库符合这一查询结果（”fMRI”, “functional MRI” OR “functional magnetic resonance imaging”）的引文数量1.1.1 血流量与神经活动通常使用的fMRI技术所基于的原理是，如果大脑内神经活动增强，相应脑区的血流量就会增加。

这一现象已发现一百多年，但其背后的机制却并不明确。

更有趣的是，对活动脑区的供血量所承载的氧分子要多于活动神经元实际耗氧量。

因此，神经活动引起的血流量增加会带来相关区域血氧含量的提高。

fMRI信号正是取决于血氧水平变化，因而被称为血氧水平依赖信号，即BOLD (Blood Oxygenation Level Dependent)信号。

图1.2展示了一个血液动力学响应的例子，即由短暂神经活动所引起的的血流量的增加。

BOLD fMRI的血液动力学响应有两个主要特点，这两个特点决定了数据的分析方法。

一，血液动力学响应较慢。

神经活动也许仅持续几毫秒，但血流量达到其峰值需要5秒左右，然后在15-20秒返回至基线。

二，血液动力学响应可以大致看作线性非时变系统(Cohen, 1997; Boynton et al., 1996; Dale, 1999)。