Pubmed Xml To Other Format, Such As Enw

Question

[xiaoronglv]

Hi，guys

I want to convert PubMed xml to other format, For example:

• endnote enw file
• RIS format
• BibTex Format

Are there Projects in github that convert PubMed xml file to other format?

I would appreciate if could help me.

thanks

---

PS

PubMed xml: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=22805184&rettype=xml

Endnote enw:

%0 Journal Article

%A Hummer DL

%A Peckham EM

%T Estradiol acts during a post-pubertal sensitive period to shorten free-running circadian period in male Octodon degus

%J The European journal of neuroscience

.........

[Pierre Lindenbaum]

Your URL is not an article record but a journal

[xiaoronglv]

sorry,I will correct it.

[Pierre Lindenbaum]

your article is not indexed in pubmed.

Answer 1

[Pierre Lindenbaum]

The idea is to use a XSLT styleheet to transform the XML/Pubmed:

Something like (Biostar is still broken for visualizing the XML, click on "revisions" below to see the real stylesheet):

	<?xml version='1.0' encoding="ISO-8859-1"?>
	<xsl:stylesheet
	xmlns:xsl='http://www.w3.org/1999/XSL/Transform'
	version='1.0'
	>
	<xsl:output method='text' encoding="UTF-8"/>
	<xsl:template match="/">
	<xsl:apply-templates select="//PubmedArticle"/>
	</xsl:template>
	<xsl:template match="PubmedArticle" >
	<xsl:text>TY - JOUR
	</xsl:text>
	<xsl:apply-templates select="MedlineCitation/Article/AuthorList/Author"/>
	<xsl:apply-templates select="MedlineCitation/Article/ArticleTitle"/>
	<xsl:text>
	</xsl:text>
	</xsl:template>
	<xsl:template match="ArticleTitle" >
	<xsl:text>TI - </xsl:text>
	<xsl:value-of select="."/>
	<xsl:text>
	</xsl:text>
	</xsl:template>
	<xsl:template match="Author" >
	<xsl:text>AU - </xsl:text>
	<xsl:value-of select="LastName"/><xsl:text> </xsl:text><xsl:value-of select="Initials"/>
	<xsl:text>
	</xsl:text>
	</xsl:template>
	</xsl:stylesheet>

view raw biostar49683.xsl hosted with ❤ by GitHub

Result:

$ xsltproc --novalid input.xsl "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=22805184&rettype=xml"

TY  - JOUR
AU  - Hummer DL
AU  - Peckham EM
AU  - Lee TM
TI  - Estradiol acts during a post-pubertal sensitive period to shorten free-running circadian period in male Octodon degus.

Answer 2

[Leonor Palmeira]

Have you tried looking a this post: http://www.biostars.org/post/show/14051/how-to-generate-a-bibtex-file-from-pmids

Apart from that, the example you provide is a bit odd: the Pubmed XML and Endnote format you provide don't refer to the same paper.

[xiaoronglv]

thanks for your advice, I have corrected the enw file. :smile:

Answer 3

[Neilfws]

There are repositories other than Github ;)

and at one of them, Sourceforge, you will find bibutils. It's a mature software project with tools to interconvert between many bibliographic formats, including Pubmed XML.

[xiaoronglv]

the bibutils is great thanks