scribble

吕小荣

Blog Friends RSS About

PubMed to EndNote by enw file

23 July, 2012

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

    取…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: [email protected].

    数据取自这个节点

    <Affiliation>Shanghai Geriatric Institute of Chinese Medicine, Shanghai 200031, China; E-mail: [email protected].</Affiliation>