scribble

吕小荣

Blog Friends RSS About

PubMed to EndNote by enw file

Published on 2012-07-23

enw文件是参考文献通用标准,与各种文献管理软件兼容好。比如这个文件test.enw,下载后双击即可导入到参考文献管理软件endnote、papers等。enw文件会调用EndNote中对应filter(EndNoter Import.enf),将不同字段的内容填充到endnote中对应的字段。Mac下的参考文献管理软件Papers也是采用这种原理。科研著作有多种类型,journal article、book、conference paper等。由于PubMed为医学文献数据库,因此类型全部为journal article。 本文重点描述,如何将PubMed中的文献导出为正确的enw文件。

编码:utf8 扩展名:enw

%0 Journal Article
%A Author
%J Journal
%C {IGNORE}
%D Year
%E {IGNORE}
%F Label
%G Language
%H Translated Author
%I {IGNORE}
%K Keywords
%L Call Number
%M Accession Number
%N Issue
%O Alternate Journal
%P Pages
%Q Translated Title
%R DOI
%S {IGNORE}
%T Title
%U URL
%V Volume
%W Database Provider
%X Abstract
%Y {IGNORE}
%Z Notes
%1 Legal Note
%2 PMCID
%3 {IGNORE}
%4 {IGNORE}
%6 {IGNORE}
%7 Epub Date
%8 Date
%9 Type of Article
%? {IGNORE}
%@ ISSN
%! Short Title
%# {IGNORE}
%$ {IGNORE}
%] {IGNORE}
%& Start Page
%( Original Publication
%) Reprint Edition
%* Reviewed Item
%+ Author Address
%^ Caption
%> File Attachments
%< Research Notes
%[ Access Date
%= {IGNORE}
%~ Name of Database

XML是自我描述性文档,PubMed中的每篇文献都有xml版本,我们可以基于XML生成enw文件。本文中以Chinese herbal medicine for patients with mild to moderate Alzheimer disease based on syndrome differentiation: a randomized controlled trial这篇文章为例,介绍整个转化流程。

XML的获取

利用NCBI的公共接口Eutility获取该文献的xml文件

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=22805083&rettype=xml

备注:
db=PubMed 数据库为pubmed,
id=22805083 id为22805083对应的文献。

生成enw文件

  1. 文章类型(%0)

所有pubmed中导出的著作类型都是journal article,因此默认的值:

%0 Journal Article
  1. 作者

    1. 如果有多个作者,每个作者开头用%A,如:
    %A 张三
    %A 李四 %A 吕小荣
    1. 作者(%A)Author

      这篇文献http://www.ncbi.nlm.nih.gov/pubmed/22805083 有12个作者,作者在endnote中保存的格式为:姓+ForeName首字母,ForeName首字母之间用“点”隔开。

           Lin, S.M.
           Zhou, R.Q.
           Tang, W.J.
           Huang, P.X.
           Dong, Y.
           Wang, J.
           Yu, Z.H.
           Chen, J.L.
           Wei, L.
           Xing, S.L.
           Cao, H.J.
           Zhao, H.B.
      

    如果采用这种样式排版,文章中出现的引文样式丑陋,如下所示:

     Lin S.M.,Zhou R.Q.,Tang W.J., et al. Chinese herbal medicine for patients with mild to moderate Alzheimer disease based on syndrome differentiation: a randomized controlled trial. Zhong Xi Yi Jie He Xue Bao. 2012 Jul;10(7):766-76.
    

    然而大多数杂志引文的排版格式为:姓+Initials

     Lin SM, Zhou RQ, Tang WJ, et al. Chinese herbal medicine for patients with mild to moderate Alzheimer disease based on syndrome differentiation: a randomized controlled trial. Zhong Xi Yi Jie He Xue Bao. 2012 Jul;10(7):766-76.
    

    因此这个作者对应的正确板式应该为: Lin SM(LastName + Initials)

     <Author ValidYN="Y">
     <LastName>Lin</LastName>
     <ForeName>Shui-Miao</ForeName>
     <Initials>SM</Initials>
     </Author>
    
  2. 期刊 (%J)Journal

    引文格式一般用杂志简写,因此这个字段应为此杂志的ISO abbreviation

    %J Zhong Xi Yi Jie He Xue Bao
  3. 年(%D)Year

     %D 2012
    

    取这个节点的数据: Article => Journal => ISSN => JournalIssue =>PubDate => Year

     <Article PubModel="Print">
     <Journal>
     <ISSN IssnType="Print">1672-1977</ISSN>
     <JournalIssue CitedMedium="Print">
     <Volume>10</Volume>
     <Issue>7</Issue>
     <PubDate>
     <Year>2012</Year>
     <Month>Jul</Month>
     </PubDate>
     </JournalIssue>
     <Title>Zhong xi yi jie he xue bao = Journal of Chinese integrative medicine</Title>
     <ISOAbbreviation>Zhong Xi Yi Jie He Xue Bao</ISOAbbreviation>
     </Journal>
     <ArticleTitle>[Chinese herbal medicine for patients with mild to moderate Alzheimer disease based on syndrome     differentiation: a randomized controlled trial].</ArticleTitle>
     <Pagination>
     <MedlinePgn>766-76</MedlinePgn>
     </Pagination>
     </Article>
    
  4. 语言(%G)Language

     %G eng
    
     <Language>eng</Language>
    
  5. 期(%N)Issue

     %N 7
    

    取这个节点的数据: Article => Journal => ISSN => JournalIssue =>Issue

       <Article PubModel=”Print”>
       <Journal>
       <ISSN IssnType=”Print”>1672-1977</ISSN>
       <JournalIssue CitedMedium=”Print”>
       <Volume>10</Volume>
       <Issue>7</Issue>
       <PubDate>
       <Year>2012</Year>
       <Month>Jul</Month>
       </PubDate>
       </JournalIssue>
       <Title>Zhong xi yi jie he xue bao = Journal of Chinese integrative medicine</Title>
       <ISOAbbreviation>Zhong Xi Yi Jie He Xue Bao</ISOAbbreviation>
       </Journal>
       <ArticleTitle>[Chinese herbal medicine for patients with mild to moderate Alzheimer disease based on syndrome      differentiation: a randomized controlled trial].</ArticleTitle>
       <Pagination>
       <MedlinePgn>766-76</MedlinePgn>
       </Pagination>
       </Article>
    
  6. 页码(%P)Pages

     %P Pages
    

    取这个节点的数据: Article => Pagination => MedlinePgn

     <Article PubModel=”Print”>
     <Journal>
     <ISSN IssnType=”Print”>1672-1977</ISSN>
     <JournalIssue CitedMedium=”Print”>
     <Volume>10</Volume>
     <Issue>7</Issue>
     <PubDate>
     <Year>2012</Year>
     <Month>Jul</Month>
     </PubDate>
     </JournalIssue>
     <Title>Zhong xi yi jie he xue bao = Journal of Chinese integrative medicine</Title>
     <ISOAbbreviation>Zhong Xi Yi Jie He Xue Bao</ISOAbbreviation>
     </Journal>
     <ArticleTitle>[Chinese herbal medicine for patients with mild to moderate Alzheimer disease based on    syndrome     differentiation: a randomized controlled trial].</ArticleTitle>
     <Pagination>
     <MedlinePgn>766-76</MedlinePgn>
     </Pagination>
     </Article>
    
  7. DOI(%R)

     %R 10.1007/s00248-011-9913-9
    

    取ArticleIdList => ArticleId (IdType=”doi”)的值

        <ArticleIdList>
        <ArticleId IdType=”doi”>10.1007/s00248-011-9913-9</ArticleId>
        <ArticleId IdType=”pubmed”>21805083</ArticleId>
        </ArticleIdList>
    
  8. 标题 (%T)Title

     %T Chinese herbal medicine for patients with mild to moderate Alzheimer disease based on syndrome differentiation: a randomized controlled trial.
    

    取Article => ArticleTitle 中的值,如果标题被中括号包裹,则去掉两端的中括号。

     <ArticleTitle>[Chinese herbal medicine for patients with mild to moderate Alzheimer disease based on syndrome differentiation: a randomized controlled trial].</ArticleTitle>
    
  9. 超链接(%U)URL

    每个URL另起一行

    %U http://pubmed.cn/22805083
    %U http://openurl.ebscohost.com/linksvc/linking.aspx?
    

    URL应该包括两部分:

    1. PubMed中的链接 http://pubmed.cn/22805083
    2. 该文献linkout的超链接
  10. 卷(%V)Volume

    %V 10
    

    取Article => Journal => JournalIssue => Volume中的数据

  11. 数据提供方(%W)

    %W PubMed.cn
    
  12. 摘要(%X)abstract

    %X Abstract
    

    节点内的数据

  13. ISSN (%@)

    ISSN多个时的处理方法如下:

    %@ 1872-7972 (Electronic)
    %@ 1872-7972 (Print)
    %@ 0304-3940 (Linking)
    
  14. 作者单位 (%+)Author Address

    %+ Shanghai Geriatric Institute of Chinese Medicine, Shanghai 200031, China; E-mail: trastayl@hotmail.com.
    

    数据取自这个节点

    <Affiliation>Shanghai Geriatric Institute of Chinese Medicine, Shanghai 200031, China; E-mail: trastayl@hotmail.com.</Affiliation>
    

吕小荣 at 00:00
Edit this page