Getting Tab-Delimited Pmids And Abstracts From Pubmed

Question

[Ryan D]

I have a list of 4000+ PMIDs from a meta-analysis query for which I'd like to pull abstracts from Pubmed. I can get title, description, details, nd other items using Batch Entrez http://www.ncbi.nlm.nih.gov/sites/batchentrez? But I can't find a way to get PMIDs and abstracts one per line. Is there a way to do this that doesn't require me to break up my query?

Answer 1

[Nakao]

If your list of PMIDs is in a file, pmids.txt with one PMID per line, here's a shell script with TogoWS solution:

for i in `cat pmids.txt`; do echo -n $i;ruby -e 'print "\t"'; curl "http://togows.dbcls.jp/entry/ncbi-pubmed/$i/ab"; done

[Neilfws]

I keep a list of searchable fields for Entrez databases at a public Dropbox: http://dl.dropbox.com/u/1304874/entrez/index.html.

[Nakao]

You can see the available entry fields at http://togows.dbcls.jp/entry/ncbi-pubmed?fields , and the available data sources at http://togows.dbcls.jp/entry/ . More details: http://togows.dbcls.jp/site/en/rest.html

[Ryan D]

Good lord, that is an impressive one-liner.

So, in addition to .ab and .pmid, where is there a list of all the suffixes and their corresponding fields which can be pulled from Medline or other NCBI databases in this manner?

Answer 2

[Pierre Lindenbaum]

Once you get all your articles, click on the button send-to /File/XML and save the articles as XML.

Then apply this XSLT-stylesheet ( xsltproc --novalid stylesheet.xsl pubmed_result.txt )

<xsl:stylesheet version="1.0" xmlns:xsl="&lt;a href=" http:="" www.w3.org="" 1999="" XSL="" Transform"="" rel="nofollow">http://www.w3.org/1999/XSL/Transform" 
    >

<xsl:output method="text"/>
<xsl:template match="/">
    <xsl:for-each select="/PubmedArticleSet/PubmedArticle">
        <xsl:value-of select="MedlineCitation/PMID"/>
        <xsl:text>  </xsl:text>
        <xsl:value-of select="normalize-space(MedlineCitation/Article/Abstract)"/>
        <xsl:text>
</xsl:text>
    </xsl:for-each>
</xsl:template>

</xsl:stylesheet>

[Ryan D]

Thanks, Pierre. This worked on the file I had. I had pulled an XML file but was unaware of this xsltproc command. I'd not worked with XML files before.

Answer 3

[Neilfws]

Some parsing is required in cases like this.

If your list of PMIDs is in a file, pmids.txt with one PMID per line, here's a BioRuby solution:

#!/usr/bin/ruby

require "rubygems" # ruby1.8
require "bio"

Bio::NCBI.default_email = "[e-mail]"

File.read("pmids.txt").each do |line|
  article = Bio::PubMed.query(line)
  medline = Bio::MEDLINE.new(article)
  puts "#{medline.pmid}\t#{medline.ab}"
end

[Ryan D]

Neil, this is a quite elegant solution. The more I learn about ruby, the more I am impressed by it.