Getting List Of Pmcids From Pubmed Central

Question

[Yogesh Pandit]

Hi,

For a given query, how can I retrieve a list of all the PMCIDs, from Pubmed Central, (using Java/Perl) that are returned.

Thanks

[Venkat Raghavan]

@pierre,neilfws,Alex

The question was how to retrieve PMC ids and not PM ids - Pubmed Central id are completely DIFFERENT from Pubmed Ids. None of the above code will get the PMC ids.

[Neilfws]

Incorrect I'm afraid. In all of the above code, the database specified is "pmc" Also, your comment is not an answer.

[User56]

EUtils also offer converting PMID into PMC ID

Answer 1

[Alex]

And a BioPython example:

#!/usr/bin/env python
from Bio import Entrez

Entrez.email = "[e-mail]"
handle = Entrez.esearch(db="pmc", term="colorectal[TITL] AND human[ORGN]")
record = Entrez.read(handle)

print record["IdList"]
['2946291', '2883131', '2837015', '2438340', 
'2134920', '1531685', '194569', '153461', '1506207']

For more information, see here.

Answer 2

[Pierre Lindenbaum]

Use NCBI EUtils to get your articles PMCID. e.g:

http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pmc&term=Rotavirus

returns:

[HTML]
http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">
[HTML]
  [HTML]4652[HTML]
  [HTML]20[HTML]
  [HTML]0[HTML]
  [HTML]
        [HTML]1852122[HTML]
        [HTML]2488191[HTML]
        [HTML]2921258[HTML]
        [HTML]2268446[HTML]
            (...)

You can then extract those Ids using XSLT or SAX, or DOM or Stax or whatever...

Answer 3

[Neilfws]

As Pierre says, the EUtils are your friend. You can either work with the raw XML, as in his example, or use your language of choice. The major Bio* libraries (Bioperl, BioPython, BioRuby) all have libraries for working with EUtils. Search them for Bio::DB::EUtilities, Bio.entrez and Bio::NCBI::REST, respectively.

Here's a Bioperl example:

#!/usr/bin/perl -w
use strict;
use Bio::DB::EUtilities;

my $factory = Bio::DB::EUtilities->new(-eutil  => 'esearch',
                                       -db     => 'pmc',
                                       -term   => 'colorectal[TITL] AND human[ORGN]',
                                       -email  => '[e-mail]',
                                       -retmax => 10);

my @ids = $factory->get_ids;
print "@ids\n";

[2946291 2883131 2837015 2438340 2134920 1531685 194569 153461 1506207]

And here's a BioRuby example:

#!/usr/bin/ruby
require "rubygems"
require "bio"

Bio::NCBI.default_email = "[e-mail]"
ncbi   = Bio::NCBI::REST.new
search = ncbi.esearch("human[ORGN] colorectal[TITL]",
                     {"db" => "pmc", "retmax" => 10})

puts search.inspect
["2946291", "2883131", "2837015", "2438340", "2134920",
 "1531685", "194569", "153461", "1506207"]

You'll note that despite retmax = 10, both of these returned 9 results :-)