pubmed使用介绍资料

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2019-PubMed检索示例-作者单位的检索-文档资料

5.修正检索策略
检出结果数量发生了很大的变化。
此次检索我们没有再次进入Limits选择限定条件。因为限定条件一旦选定，若不取消，则在后面的检索中始终存在。因此，请注意：检索完成后，若不再需要此限定条件，一定要点击“Remove”去除掉限定条件；若限定条件发生变化，则点击“Change”重新进入Limits进行修改。
检查details，没有问题。
*更简单的方法
• 选好限定条件后利用高级检索来进行检索词的输入。因为高级检索也可进行字段限定检索
点击进入高级检索
①选择入口字段 ②输入检索词
Chongqing medical university
③点击index按钮
④点击AND按钮
①选择入口字段 ②输入检索词
小结
• 检索时一定要注意选词！ PubMed的词语自动转换功能主要是针对主题内容的检索而言的，如果是检索某机构作者发表的文献，一定要事先了解这个机构的名称有哪些写法。不同写法之间用OR连接。可考虑使用Index功能。
• 如果是检索某一主题内容的文献，可以不用考虑同义词，直接在基本检索状态输入检索词就可以了（但词组检索不能加引号，否则将关闭自动转换功能）。
Chongqing medical university
③点击index按钮
⑤输入其他检索词
Chongqing university of medical science
⑥点击index按钮
⑧点击OR按钮
⑦选择需要的词
发现我们刚刚还漏掉了另一个检索词
⑨点击Search或Preview
若点击Preview，则不直接显示检索具体结果，而是在下方的检索史（Search History）中预览结果数量。请比较#2和#4的检索结果。由于我们前面进行的检索（#2）漏掉了一个检索词，导致检索结果少了202篇。

PubMed简介及使用说明

PubMed简介及使用说明壹、简介PubMed为美国国家医学图书馆的美国国家生技资讯中心(NCBI)所制作之生物医学相关文献的书目索引摘要型资料库，目前收录1950年以来约1400多万笔生物医学相关书目资料，并提供部分免费及付费全文连结服务，需要收费的全文，读者可自行与出版社接洽。

较之于MEDLINE资料以生物医学、生命科学、生化学、行为科学为主，PubMed 资料库范围更涵盖了如下内容：1. 对于超出学科范围(如：资讯科学、航太科学) 的特定生命科学、医学、化学相关之期刊文章都会收录于本资料库中；2. 收录即将出版的医学论文；3. 已由NLM审核通过并已由PubMed Central典藏的全文文献亦收录之。

美国国家生技资讯中心(NCBI)制作了一系列的生物医学资料库如下：1.PubMed：生物医学文献书目索引摘要资料库。

2.Nucleotide：包含GenBank、RefSeq、PDB资料库中的人类基因序列资料。

3.Protein：整合了SwissProt、PIR、PRF、PDB、GenBank及RefSeq资料库中的资料，并可参照Taxonomy资料库，了解特定种类的蛋白质的在资料库中分类状况的相关说明。

4.Structure：分子构造资料库。

5.Genome：基因组合序列资料库。

6.PopSet：可查询某族群的基因序列，了解该族群演进之相关资料。

7.OMIM：遗传学资料库。

8.Taxonomy：在NCBI基因资料库中提及的微生物的核酸或蛋白质序列的分类状况之相关说明。

9.Books：收录C. elegans II.、Introduction to Genetic Analysis. 7th ed.、ModernGenetic Analysis.、Molecular Biology of the Cell. 3rd ed.、Molecular Cell Biology. 4th ed.、Retroviruses.等六本书。

一PubMed数据库简介-文档资料

四、PubMed的基本检索功能（一）
自动词语匹配
PubMed 能自动利用它的“自动词语匹配
”功能将重要的词语结合在一起，并将不规范的词语转换成规范的用词。如：输入vitamin c common cold，系统会将自动
转换成 (“ascorbic acid”[MeSH Terms] OR vitamin c[Text Word]) AND (“common cold”[MeSH Terms] OR common cold [Text Word]) 进行检索。这种处理能使检索结果更精确和全面。
பைடு நூலகம்
四、PubMed的基本检索功能
词语检索及自动词语匹配作者姓名检索杂志名称检索截词检索短语检索逻辑运算符检索
四、PubMed的基本检索功能（一）
词语检索及自动词语匹配
在检索框中键入一到多个检索词，按
“GO”键，即显示检索结果。 “clear” 按钮可以帮你清除查询框中的内容，然后开始一个新的查询。
杂志名检索

在检索框中键入杂志全名molecular biology of the cell 也可以直接键入Medline的期刊标准缩写形式，如：mol boil cell，键入刊物的ISSN(国际标准出版物代码）进行检索，如1059-1524。 Cell transplantation [ta]
PubMed辅助检索工具
Limits （限制功能） Preview/Index（预览/索引） History（检索史） Clipboard（剪贴板或文件夹） Details（明细栏）
Journal Browser-杂志浏览器
服务功能
•MeSH Browser-主题词浏览器 •Citation Matcher-在表格输入刊物的引文信息来定位特定文章。 •Clinical Queries-与临床相关的疗法，诊断，病因，预后

pubmed检索步骤 -回复

pubmed检索步骤-回复Pubmed是世界上最大的医学文献数据库之一，提供了大量的生物医学文献资料，包括期刊文章、会议摘要、学位论文等。

Pubmed的使用可以帮助研究人员快速检索到相关的医学文献，有效地支持他们的科研工作。

本文将介绍使用Pubmed进行文献检索的步骤，并以"乳腺癌治疗的最新进展"为例进行说明。

第一步：进入Pubmed网站首先，我们需要打开网页浏览器，输入"第二步：选择搜索关键词在Pubmed的首页上，我们可以看到一个搜索框。

输入"乳腺癌治疗的最新进展"作为关键词进行搜索。

在这里，我们需要注意的是，关键词的选择应该准确反映我们所关注的研究主题，以便能够检索到相关的文献。

第三步：筛选搜索结果点击搜索按钮后，Pubmed会根据关键词进行检索，并列出包含这些关键词的文献列表。

在这里，我们可以看到大量的搜索结果。

为了筛选出最相关的文献，我们可以使用Pubmed的搜索筛选工具。

在搜索结果页面的左侧，有一栏搜索筛选工具。

我们可以根据不同的筛选条件，比如出版日期、文章类型、研究主题等进行进一步的筛选。

以乳腺癌治疗的最新进展为例，我们可以选择筛选条件为"出版日期"，选择"最近五年"，以获取最近的研究进展。

第四步：查看摘要和全文在筛选出相关的文献后，我们可以点击文献标题或摘要，进一步查看文献的详细信息。

在这里，我们可以通过查看摘要了解到文献的研究内容、方法和主要结论。

如果我们对某篇文献特别感兴趣，想要获取全文信息，可以通过点击链接或按钮，获取全文或者转至相关网页。

然而，需要注意的是，Pubmed并不提供所有文献的全文，有些文章可能需要通过其他渠道获得。

第五步：导出文献信息在Pubmed上查到的文献信息可以方便地导出到其他文献管理软件，如EndNote等。

在详细信息页面，Pubmed提供了一个"导出"按钮，点击后可以选择导出格式，然后将文献信息导出到所选的文献管理软件中。

NCBI-PubMed-检索简介与检索技巧集锦

NCBI PubMed 检索简介与检索技巧集锦注：在本文中的叙述中，所有输入PubMED检索框中的内容均用<>符号括起来，如以基因治疗为主题词检索，在检索框中的输入内容表示为<"Gene Therapy"[MESH]>。

PubMed简介PubMed是由隶属于美国国家卫生部（NIH, National Institues of Health）的国家医学图书馆（NLM, Nationa Library of Medicine）下属的国家生物技术信息中心（NCBI, National Center for Biotechnology Information）提供，可通过NCBI网站的Entrez检索系统（Entrez retrieval system）进行MEDLINE和PreMEDLINE引文数据库的在线免费检索。

此外，PubMed还提供引文与其它数据库的接入服务，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，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。

Entrez检索系统是NCBI在线提供的一类基于文字进行搜索与索取的检索系统，可检索NCBI网站的主要数据库，如PubMed，核酸与蛋白序列，基因组序列，蛋白结构，OMIM等等。

PubMed是一类提供生物医学文献资料检索的数据库，此外，它还针对网上资源，提供全文地址及其它相关的NCBI提供的网上资源，如核酸蛋白序列、OMIM入口等，以及其它生命科学数据库。

其文献内容的提供方式，由各期刊出版商在期刊发表前可发表时提供给NCBI。

如果该出版商有网站，则NCBI会提供相应的网络出口。

MEDLINE 及PubMed引文数据库中的新条目在每周周二至周六每日更新。

PubMed服务内容概括基于互联网及PreMEDLINE引文数据库免费检索系统。

NCBIPubMed检索简介与检索技巧集锦

NCBI PubMe‎d检索简介与‎检索技巧集‎锦注：在本文中的‎叙述中，所有输入P‎u bMED‎检索框中的‎内容均用<>符号括起来‎，如以基因治‎疗为主题词‎检索，在检索框中‎的输入内容‎表示为<"Gene Thera‎p y"[MESH]>。

PubMe‎d简介PubMe‎d是由隶属‎于美国国家‎卫生部（NIH, Natio‎n al Insti‎tu es of Healt‎h）的国家医学‎图书馆（NLM, Natio‎na Libra‎ry of Medic‎i n e）下属的国家‎生物技术信‎息中心（NCBI, Natio‎n al Cente‎r for Biote‎c hnol ‎o g y Infor‎m a tio‎n）提供，可通过NC‎BI网站的‎E n tre‎z检索系统‎（E ntre‎z retri‎e val syste‎m）进行MED ‎L I NE和‎P reME‎D LINE‎引文数据库‎的在线免费‎检索。

此外，PubMe‎d还提供引‎文与其它数‎据库的接入‎服务，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，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。

Entre‎z检索系统‎是NCBI‎在线提供的‎一类基于文‎字进行搜索‎与索取的检‎索系统，可检索NC‎BI网站的‎主要数据库‎，如PubM‎ed，核酸与蛋白‎序列，基因组序列‎，蛋白结构，OMIM等‎等。

PubMe‎d是一类提‎供生物医学‎文献资料检‎索的数据库‎，此外，它还针对网‎上资源，提供全文地‎址及其它相‎关的NCB‎I提供的网‎上资源，如核酸蛋白‎序列、OMIM入‎口等，以及其它生‎命科学数据‎库。

PubMed使用攻略

资料仅供参考,不当之处，请联系改正。
主要内容
一、PubMed简介二、检索途径和方法三、检索结果处理
四、其他辅助检索
五、免费获取全文
华中科技大学同济医学院医药卫生管理学院
资料仅供参考,不当之处，请联系改正。
一、PubMed简介
▪ 1.PubMed基本情况 ▪ 2.PubMed的由来 ▪ 3.PubMed的数据范围 ▪ 4.PubMed的特点 ▪ 5.PubMed主页
资料仅供参考,不当之处，请联系改正。
一、PubMed简介
3.PubMed的数据范围
MEDLINE PreMedline
出版商提供的书目信息与NCBI其它数据库的链接
华中科技大学同济医学院医药卫生管理学院
资料仅供参考,不当之处，请联系改正。
MEDLINE数据库简介
3.1 MEDLINE基本情况
▪ 出版：美国国家医学图书馆（ National
华中科技大学同济医学院医药卫生管理学院
资料仅供参考,不当之处，请联系改正。
▪ 学科范围：
▪ 基础生命科学 ▪ 生物科学 ▪ 组织学 ▪ 心理学 ▪ 农业 ▪ 医技工业学
临床生命科学解剖学化学与药物社会医学医技设备学医学信息学
使用词表：MeSH（医学主题词表）
华中科技大学同济医学院医药卫生管理学院
华中科技大学同济医学院医药卫生管理学院
资料仅供参考,不当之处，请联系改正。
一、PubMed简介
▪ 1.PubMed基本情况
▪ PubMed是美国NLM所属的国家生物技术信息
中心（NCBI）开发的一个以Web方式向用户提供服务的生物医学文献检索系统，是继 MEDLINE数据库国际联机检索和光盘检索之后推出的一种网络免费检索方式。

PubMed检索系统-文档资料

2个字母在词后时， PubMed 就会到著者索引中查找。
若在上述四个表或索引中仍未找到相匹配的词， PubMed 就将短语分开，用AND将短语中的单个词连接起来在全部字段中查找，直到找到相应的词为止。例：pressure point
（“pressure”[MeSH Terms] OR “pressure”[All Fields]）
二、 PubMed主页简介
PubMed主页
二、 PubMed主页简介
主页分检索区、主要功能区及辅助功能区三部分。
检索区：基本检索、高级检索和帮助。
主要功能区：使用介绍、 PubMed工具及更多资源。
二、 PubMed主页简介
辅助功能区：指南、其他数据库、常用数据库、特色数据库及相关信息
三、 PubMed主要特点
AND point[All Fields]
三、 PubMed主要特点
㈡截词检索用截词符“ * ”表示。截词检索只限于单词，对词组无效。例如：flavor* flavored ， flavorful ， flavoring等㈢短语检索又称强制检索，即对检索词加上双引号（“ ”），把检索词作为一个整体检索，关闭自动词语匹配功能。例：“single cell”
三、 PubMed主要特点
㈣布尔逻辑检索
布尔逻辑运算符必须大写 ANFra bibliotek OR NOT
优先级为：（）＞NOT＞AND＞OR
三、 PubMed主要特点
㈤限定检索
PubMed在首次检索的基础上，可以根据检索需求实现二次检索界面的限定检索：包括文本呈现方式（摘要、免费全文、全文）、出版日期、物种（人或其他动物）、文献类型（临床实验、随机对照实验、综述、系统综述等）、语言和年龄等。

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名词解释

pubmed名词解释
pubmed
pubmed(含义、定义)一般指按照某一特定主题搜集、整理和比较相关文献。

pubmed(内容、形式)泛指特定研究领域的文献内容，包括文献的信息、资料和研究方法等。

pubmed(性质、状态)是反映出某一事
物特征或属性的词汇，可以用来描述一个事物的行为，也可以用来指一种特定状态，例如“她住在寄宿家庭”中的“寄宿家庭”就是“性质”的意思。

pubmed(语言、文化)指人们在某个特定时期的语言
习惯或者风俗习惯，还可以指文化氛围、精神追求等，可以用于描述语言习惯或者人们的风俗习惯。

1.通过制定指标来评价所发表的文献，衡量论文在学术上的贡献，或反映某一研究领域在科学或技术上的水平。

2.通过文献计量方
法来收集并分析文献数据，确定某一课题或者专题的文献数量及其与有关因素之间的关系，如：相关度、时间序列分析、主成分分析、偏相关分析、系统聚类分析、网络分析、相关分析、中心极限定理等。

3.利用文献计量的统计分析方法来判断、监测和控制文献计量的使用情况，确保文献计量与学术成果相符合。

2.包括对文献的搜集、整理、加工、分类、检索、阅读等系统性研究。

3.通过文献计量方法来判断、监测和控制文献计量的使用
情况，确保文献计量与学术成果相符合。

2.既包括了实证研究，
又包括了规范研究。

3.研究主要在自然科学中进行，当然也有社
会科学研究。

3.一般是先在本学科的领域里探索，再将已获得的成果运用到另外的领域。

1.通过数据库技术建立起来的，拥有全面资料的巨大网络，包括联机文摘数据库、全文数据库、期刊全文数据库、图书全文数据库、专利全文数据库等。

在pubmed中获取全文的方法

在pubmed中获取全文的方法1. 背景介绍Pubmed是一种由美国国立卫生研究院提供的生命科学和生物医学领域的数据库，涵盖了广泛的期刊文献和临床医学资料。

在进行科研和学术研究过程中，许多研究者需要在Pubmed中获取全文来支撑自己的研究工作。

在本文中，我们将介绍在Pubmed中获取全文的方法，帮助广大科研者更加高效地获取所需文献。

2. 方法步骤2.1 进入Pubmed全球信息站我们需要打开浏览器，输入Pubmed的全球信息站（xxx），进入Pubmed全球信息站。

2.2 输入搜索关键词在全球信息站的搜索框中输入所需查找的文献关键词，点击搜索按钮进行检索。

2.3 进行筛选和排序Pubmed会返回相关的文献列表，我们可以根据年代、出版物类型、作者、语言等条件进行筛选和排序，以便更快地找到需要的文献。

2.4 确认文献信息在找到目标文献后，我们需要点击文献标题，进入文献详细信息页面。

在该页面中，我们可以查看文献的摘要、作者、期刊、出版日期等信息，并确认是否需要获取全文。

2.5 点击获取全文在确认需要获取全文后，我们可以看到页面上有“Full Text Links”或“Free Full Text”等按钮，点击该按钮即可进入全文下载页面。

2.6 下载全文在全文下载页面，我们可以选择下载格式（如PDF或HTML），点击相应的信息进行下载，即可获取全文。

3. 注意事项在使用Pubmed获取全文的过程中，需要注意一些事项，以保证获取的文献的准确性和可靠性。

3.1 确认文献来源在点击获取全文前，需要确认文献来源的可靠性，避免获取到不准确或非权威的文献。

3.2 扩大检索范围有时候我们可能无法直接在Pubmed上找到所需的文献全文，这时可以尝试在其他数据库或学术搜索引擎上进行检索，扩大检索范围。

3.3 合理使用资源在获取全文时，要合理使用自己的资源，在需要时可以通过机构订购、申请文献传递或采用其他合法途径获取全文。

pubmed的使用方法

近年来，利用计算机进行文献检索已逐步代替传统的手工检索，随着Internet的普及，我们可以随时随地通过国际互联网来检索获得免费的医学文献，这是一条文献检索新捷径[1]，特别是进行MEDLINE检索，既简单又实用[2]。

现在有多个机构提供免费的网上MEDLINE检索服务，其中由美国国立医学图书馆（NLM）所属的国家生物技术信息中心（NCBI）建立的PubMed数据更新快[3]，检索系统完善，深受广大医务工作者和图书情报人员的欢迎。

由于PubMed检索系统在不断完善和加强，要快速、全面、准确地在近4千种医学期刊、1千1百万条数据中检索出符合自己要求的资料[4]，并不容易。

下面介绍最新版本（2000年9月版）的PubMed使用方法。

1. 进入PubMed在浏览器的地址栏内输入Pubmed的网址：/PubMed/后按回车键，就进入PubMed的主页，开始检索。

2. 普通检索在检索式提问框中输入一个或更多的词（例如：vitamin c common cold），然后按回车键或用鼠标点击"Go"按钮，PubMed就会利用"自动词语匹配"功能将重要的词或词组用"AND"组合在一起进行检索（见图1）。

输入的词可以是自由词、主题词、或其他指定字段。

由于主题词检索的文献更全面、更准确，应尽量使用主题词/副主题词检索。

对于某些新的技术词汇、新药、新方法、新疾病等，还没有相应的主题词时，应该用自由词检索。

3. 高级检索使用逻辑词AND, OR, NOT（例如：vitamin c OR zinc）、指定文献记录字段名称检索、使用医学主题词（MeSH）/副主题词组配格式检索，如neoplasms/diet therapy［mh］。

不久返回检索结果，检索提问框仍出现在页面顶端，并显示您刚才输入的检索词。

您可以在提问框内、点击"Details"或"Limits"按钮再修改检索词。

PubMed资料库使用介绍

全文取得途徑
PubMed Fulltext 電子資源
(.tw/ele-resource/index.html)
館藏目錄
(.tw/catalog/webpac/webpac.asp)
全國館際合作系統
(http://140.113.39.185/)
Feature Bar
Limits Preview/Index History Clipboard Details
Feature Bar -Limit
使用者可設定查詢的欄位、附摘要的文獻、出版品的類型、語文、主題類別、研究對象年齡層、研究對象、性別、系統最近更新時間、出版時間等。
Feature Bar –Preview/Index
Journals Database MeSH Brower Single Citation Clinical Queries
PubMed Services—Journals Brower
可從「題名」、「ISSN」、「刊名縮寫」查詢期刊的出版資訊。如下：
PubMed Services—Single Citation Matcher
Introduction—Homepage
資料庫選擇輔助說明 PubMed服務項目檢索 Feature Bar功能快捷列
About Entrez
Entrez是一Web-base檢索系統，用以檢索下圖所示各資料庫，只要從其中一個資料庫出發，可在檢索結果中進行相關資料庫的檢索。
Introduction—Boolean Logic
每次檢索步驟，系統都會產生一個檢索號碼，本區可看到所有的檢索步驟歷史紀錄，如要運用先前檢索的策略，可直接輸入檢索號碼並以布林邏輯加以運算，如：#1 AND #5。但此紀錄在系統未運作一小時後將被系統消除。

药学信息检索

药学信息检索药学作为一门关乎人类健康的学科，涉及到大量的药物信息。

为了从海量的文献资料中获取有效和准确的信息，药学信息检索成为药学研究者的一项重要任务。

本文将从药学信息检索的意义、常用的检索工具和技巧以及信息检索过程中的注意事项等方面进行论述。

一、药学信息检索的意义药学信息检索是药学研究和实践中必不可少的一环，它能够帮助药学工作者获取最新的研究成果和治疗方案，提高科研和临床工作的效率和质量。

具体来说，药学信息检索的意义主要体现在以下几个方面：1. 帮助了解最新研究成果：药学研究涉及到广泛的领域，包括药理学、药代动力学、药物化学等。

通过信息检索，药学研究者可以及时了解到各个领域的最新研究成果，为自己的科研工作提供参考和借鉴。

2. 促进科学交流和合作：信息检索可以帮助药学研究者找到与自己研究方向相近或者相似的学者和研究团队，从而促进科学交流和合作。

通过与其他研究者的交流合作，可以丰富自己的研究视野，提高研究的深度和广度。

3. 辅助临床决策：对于临床医生而言，药学信息检索可以提供临床治疗方案的相关文献资料，帮助医生在制定治疗方案时更科学和准确。

二、常用的药学信息检索工具和技巧在进行药学信息检索时，常用的检索工具包括数据库和检索引擎。

下面介绍几种常见的药学信息检索工具和技巧：1. PubMed：PubMed是一个由美国国立卫生研究院和国家医学图书馆共同维护的生物医学文献数据库，其中包括了大量的药学相关文献。

在使用PubMed进行信息检索时，可以使用关键词、文献类型、出版日期等进行检索。

2. Embase：Embase是一个涵盖药学、生物医学和相关领域文献的数据库，其收录范围比PubMed更广。

在使用Embase进行信息检索时，可以通过关键词、主题词、作者名等进行检索。

3. Google 学术搜索：Google 学术搜索是一个可以检索学术文献的搜索引擎，其中包括了大量的药学相关文献。

在使用Google 学术搜索进行信息检索时，可以使用关键词、作者名、出版年限等进行检索。

文献检索pubmed讲解资料PPT文档75页

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文献检索pubmed讲解资料
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