[Bioperl-l] EUtilities pubmed search with [Mesh Terms]

[Chris Fields]

Use uppercase with bools:

'anoxia[mh] AND neoplasms[mh]'

This gives me 2124 hits.  Note the URL you provided does that as well

...db=pubmed&term=anoxia[mh]+AND+neoplasms[mh]

chris

On Jun 29, 2010, at 5:41 PM, Peng Yu wrote:

> Hi,
> 
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=anoxia[mh]+AND+neoplasms[mh]
> 
> The above search returns 2124 entries. I try to use the following
> bioperl code to do the search. I got an error (see below). Could
> anybody let me know how I should modify the bioperl search code to get
> the same results?
> 
> #!/usr/bin/env perl
> 
> use strict;
> use warnings;
> use Bio::DB::EUtilities;
> 
> my $factory = Bio::DB::EUtilities->new(
>  -eutil => 'esearch',
>  -db => 'pubmed',
>  -email => 'mymail at foo.bar',
>  -term => 'anoxia[mh] and neoplasms[mh]',
>  -retmode => 'xml',
>  -retmax => 1000000,
> );
> 
> print $factory->get_retmax,"\n";
> print $factory->get_Response->content;
> 
> ############################
> 
> $ ./main.pl
> 
> --------------------- WARNING ---------------------
> MSG: NCBI esearch Errors/Warnings:
> Error : PhraseNotFound  [+and+neoplasms[mh]]Warnings : OutputMessage
> [No items found.]
> ---------------------------------------------------
> 0
> <?xml version="1.0" ?>
> <!DOCTYPE eSearchResult PUBLIC "-//NLM//DTD eSearchResult, 11 May
> 2002//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSearch_020511.dtd">
> <eSearchResult><Count>0</Count><RetMax>0</RetMax><RetStart>0</RetStart><IdList>
> 	</IdList><TranslationSet><Translation>     <From>anoxia[mh]</From>
> <To>"anoxia"[MeSH Terms]</To>
> </Translation></TranslationSet><QueryTranslation/><ErrorList><PhraseNotFound>+and+neoplasms[mh]</PhraseNotFound></ErrorList><WarningList><OutputMessage>No
> items found.</OutputMessage></WarningList></eSearchResult>
> 
> -- 
> Regards,
> Peng
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