[Bioperl-l] Error when using EUtilities to download elink with parameter LinkName=gene_pubmed
Smithies, Russell
Russell.Smithies at agresearch.co.nz
Fri Jun 11 03:52:36 UTC 2010
I suspect it's not possible without getting ASN.1 back and parsing that.
As you already have a working URL, why not use LWP?
use LWP::Simple;
my $content = get("http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?db=gene&LinkName=gene_pubmed&from_uid=6476") or die $!;
my @ids = grep(/<Id>\d+<\/Id>/,(split("\n",$content));
--Russell
> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Peng Yu
> Sent: Friday, 11 June 2010 3:27 p.m.
> To: bioperl-l at lists.open-bio.org
> Subject: [Bioperl-l] Error when using EUtilities to download elink with
> parameter LinkName=gene_pubmed
>
> Hi,
>
> I'm trying to get the pubmed ids from the following link. I use the
> code pasted at the end of the mail (the output is pasted as well).
> Note that more ids than necessary are returned. Then I try to use the
> option -dbfrom='gene_pubmed'. But it raises exceptions. Could you let
> me know how to get the correct download of the ids in the following
> page by bioperl EUtilities?
>
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?db=gene&LinkName=g
> ene_pubmed&from_uid=6476
>
> --
> Regards,
> Peng
>
> $ cat main.pl
> #!/usr/bin/env perl
>
> use strict;
> use warnings;
> use Bio::DB::EUtilities;
>
> my $factory = Bio::DB::EUtilities->new(
> -eutil => 'elink',
> -db => 'pubmed',
> -dbfrom => 'gene',
> -email => 'mymail at foo.bar',
> -id => 6476,
> );
>
> print join(',', $factory->get_ids), "\n";
> print $factory->get_Response->content;
>
> $ ./main.pl
> 19416921,19121318,17194452,16802690,16543230,16344560,16329100,15944403,15
> 522234,14724820,12477932,11340066,11329013,11003604,10903344,9092938,86092
> 17,8521865,7566098,3925457,3896809,3178143,2962903,1717481,1677636,1560017
> ,1353958,16329100,14724820,14276572,11340066,10903344,8648532,8648527,8609
> 217,8576798,8118103,7371476,6357634,6082247,5848222,5436545,5333958,507569
> 4,5041318,5015965,4952790,4742566,4579420,4164045,3925457,3807985,3553946,
> 3403721,3178143,2962903,1717481,1560017,1353958,1256470,19121318,17194452,
> 16802690,16543230,16329100,15944403,15522234,8521865
> <?xml version="1.0"?>
> <!DOCTYPE eLinkResult PUBLIC "-//NLM//DTD eLinkResult, 10 August
> 2009//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eLink_090910.dtd">
> <eLinkResult>
>
> <LinkSet>
> <DbFrom>gene</DbFrom>
> <IdList>
> <Id>6476</Id>
> </IdList>
> <LinkSetDb>
> <DbTo>pubmed</DbTo>
> <LinkName>gene_pubmed</LinkName>
> <Link>
> <Id>19416921</Id>
> </Link>
> <Link>
> <Id>19121318</Id>
> </Link>
> <Link>
> <Id>17194452</Id>
> </Link>
> <Link>
> <Id>16802690</Id>
> </Link>
> <Link>
> <Id>16543230</Id>
> </Link>
> <Link>
> <Id>16344560</Id>
> </Link>
> <Link>
> <Id>16329100</Id>
> </Link>
> <Link>
> <Id>15944403</Id>
> </Link>
> <Link>
> <Id>15522234</Id>
> </Link>
> <Link>
> <Id>14724820</Id>
> </Link>
> <Link>
> <Id>12477932</Id>
> </Link>
> <Link>
> <Id>11340066</Id>
> </Link>
> <Link>
> <Id>11329013</Id>
> </Link>
> <Link>
> <Id>11003604</Id>
> </Link>
> <Link>
> <Id>10903344</Id>
> </Link>
> <Link>
> <Id>9092938</Id>
> </Link>
> <Link>
> <Id>8609217</Id>
> </Link>
> <Link>
> <Id>8521865</Id>
> </Link>
> <Link>
> <Id>7566098</Id>
> </Link>
> <Link>
> <Id>3925457</Id>
> </Link>
> <Link>
> <Id>3896809</Id>
> </Link>
> <Link>
> <Id>3178143</Id>
> </Link>
> <Link>
> <Id>2962903</Id>
> </Link>
> <Link>
> <Id>1717481</Id>
> </Link>
> <Link>
> <Id>1677636</Id>
> </Link>
> <Link>
> <Id>1560017</Id>
> </Link>
> <Link>
> <Id>1353958</Id>
> </Link>
> </LinkSetDb>
> <LinkSetDb>
> <DbTo>pubmed</DbTo>
> <LinkName>gene_pubmed_citedinomim</LinkName>
> <Link>
> <Id>16329100</Id>
> </Link>
> <Link>
> <Id>14724820</Id>
> </Link>
> <Link>
> <Id>14276572</Id>
> </Link>
> <Link>
> <Id>11340066</Id>
> </Link>
> <Link>
> <Id>10903344</Id>
> </Link>
> <Link>
> <Id>8648532</Id>
> </Link>
> <Link>
> <Id>8648527</Id>
> </Link>
> <Link>
> <Id>8609217</Id>
> </Link>
> <Link>
> <Id>8576798</Id>
> </Link>
> <Link>
> <Id>8118103</Id>
> </Link>
> <Link>
> <Id>7371476</Id>
> </Link>
> <Link>
> <Id>6357634</Id>
> </Link>
> <Link>
> <Id>6082247</Id>
> </Link>
> <Link>
> <Id>5848222</Id>
> </Link>
> <Link>
> <Id>5436545</Id>
> </Link>
> <Link>
> <Id>5333958</Id>
> </Link>
> <Link>
> <Id>5075694</Id>
> </Link>
> <Link>
> <Id>5041318</Id>
> </Link>
> <Link>
> <Id>5015965</Id>
> </Link>
> <Link>
> <Id>4952790</Id>
> </Link>
> <Link>
> <Id>4742566</Id>
> </Link>
> <Link>
> <Id>4579420</Id>
> </Link>
> <Link>
> <Id>4164045</Id>
> </Link>
> <Link>
> <Id>3925457</Id>
> </Link>
> <Link>
> <Id>3807985</Id>
> </Link>
> <Link>
> <Id>3553946</Id>
> </Link>
> <Link>
> <Id>3403721</Id>
> </Link>
> <Link>
> <Id>3178143</Id>
> </Link>
> <Link>
> <Id>2962903</Id>
> </Link>
> <Link>
> <Id>1717481</Id>
> </Link>
> <Link>
> <Id>1560017</Id>
> </Link>
> <Link>
> <Id>1353958</Id>
> </Link>
> <Link>
> <Id>1256470</Id>
> </Link>
> </LinkSetDb>
> <LinkSetDb>
> <DbTo>pubmed</DbTo>
> <LinkName>gene_pubmed_rif</LinkName>
> <Link>
> <Id>19121318</Id>
> </Link>
> <Link>
> <Id>17194452</Id>
> </Link>
> <Link>
> <Id>16802690</Id>
> </Link>
> <Link>
> <Id>16543230</Id>
> </Link>
> <Link>
> <Id>16329100</Id>
> </Link>
> <Link>
> <Id>15944403</Id>
> </Link>
> <Link>
> <Id>15522234</Id>
> </Link>
> <Link>
> <Id>8521865</Id>
> </Link>
> </LinkSetDb>
> </LinkSet>
> </eLinkResult>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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