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#!/usr/bin/perl -w

# $Id: biblio-eutils-example.pl,v 1.1 2005/09/24 01:05:28 bosborne Exp $

=head1 NAME

 

biblio-eutils-example.pl

 

=head1 SYNOPSIS

 

Script that uses Bio::Biblio, accessing 'eutils' at PubMed.

 

As of Bioperl version 1.4 there are 3 bibliographic repositories,

stipulated by the -access argument: soap, eutils, and biofetch.

The default is 'soap'. Not all of these repositories support all

the Biblio methods nor are the contents of these repositories

necessarily the same. Choose wisely!

 

=head2 PubMed Queries

 

The syntax of the queries is the same as at PubMed, see

http://www.ncbi.nlm.nih.gov/entrez/query/Pmc/pmchelp.html#SearchFieldDescriptionsandTags

for more information on how to construct queries.

 

=head2 Parsing Results

 

Bio::Biblio will give you XML when querying eutils so you have

choose a method to parse XML. A fairly simple approach uses

XML::Twig, shown here. This example shows how query by title and

how to retrieve the titles of the abstracts found.

 

=cut

 

use strict;

use Bio::Biblio;

use XML::Twig;

 

# one-liner to get the number of abstracts found

my $num = new Bio::Biblio(-access => "eutils")->find("Osborne","authors")->

  get_count;

 

my $biblio = Bio::Biblio->new(-access => "eutils");

 

my $result = $biblio->find("brain [TI] AND MDM2 [TI]");

 

my $pmids = $result->get_all_ids;

 

my $parser = XML::Twig->new(twig_roots => {"ArticleTitle" => \&print_title} );

 

for my $pmid (@$pmids) {

        my $xml = $biblio->get_by_id($pmid);

        eval {

                $parser->parse($xml);

        };

        if ($@) {

                warn "Problem parsing PubMed $pmid XML: $!\n";

        }

}

 

sub print_title {

        my ($twig, $elt) = @_;

        print $elt->text,"\n";

        $twig->purge;

}

 

=head1 PubMed XML Example

 

<?xml version="1.0"?>

<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st November 2004//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_041101.dtd">

<PubmedArticleSet>

<PubmedArticle>

    <MedlineCitation Owner="NLM" Status="MEDLINE">

        <PMID>15815077</PMID>

        <DateCreated>

            <Year>2005</Year>

            <Month>04</Month>

            <Day>07</Day>

        </DateCreated>

        <DateCompleted>

            <Year>2005</Year>

            <Month>08</Month>

            <Day>29</Day>

        </DateCompleted>

        <Article PubModel="Print">

            <Journal>

                <ISSN>0231-5882</ISSN>

                <JournalIssue>

                    <Volume>23</Volume>

                    <Issue>4</Issue>

                    <PubDate>

                        <Year>2004</Year>

                        <Month>Dec</Month>

                    </PubDate>

                </JournalIssue>

            </Journal>

            <ArticleTitle>Rabbit liver microsomal system: study of interaction with two model N-nitrosamines and their metabolism.</ArticleTitle>

            <Pagination>

                <MedlinePgn>423-33</MedlinePgn>

            </Pagination>

            <Abstract>

                <AbstractText>Rabbit liver microsomes of control (non-treated) or animals induced either by ethanol (EtOH) or phenobarbital (PB) were incubated with N-nitrosodimethylamine (NDMA) or N-nitrosomethylaniline (NMA). Difference spectroscopy showed that NMA is bound to the substrate-binding site of cytochrome P-450 (CYP) isoforms as heme ligand in control and EtOH pre-treated microsomes. On the other hand, PB-induced microsomes exhibit with NMA substrate type of spectra. NDMA does not provide any type of binding spectra with used microsomal systems. Oxidative bio-activation of N-nitrosamines by the microsomal CYP isoforms was measured as formaldehyde formation. Analysis of reaction kinetics in control microsomes revealed, for both substrates, two values of Michaelis-Menten constant (K(m)) for, K(m) values of 0.03 and 0.13 mmol/l for NDMA, and 0.30 and 0.82 mmol/l for NMA. Induction of animals with EtOH resulted in a decrease in the K(m) value for both substrates. In contrast, PB treatment caused an elevation of K(m) value for NDMA. Based on these data, we conclude that EtOH-inducible microsomal CYP isoforms (mainly CYP2E1) are responsible for binding and N-demethylation metabolism of both studied N-nitrosamines in rabbit liver microsomal system. The role of the other CYP isoforms involved in the metabolism of mentioned N-nitrosamines is discussed.</AbstractText>

            </Abstract>

            <Affiliation>Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 128 43 Prague 2, Czech Republic. mis@natur.cuni.cz</Affiliation>

            <AuthorList CompleteYN="Y">

                <Author ValidYN="Y">

                    <LastName>Sulc</LastName>

                    <ForeName>B</ForeName>

                    <Initials>B</Initials>

                </Author>

                <Author ValidYN="Y">

                    <LastName>Kub�ckov�</LastName>

                    <ForeName>B</ForeName>

                    <Initials>B</Initials>

                </Author>

                <Author ValidYN="Y">

                    <LastName>M�slov�</LastName>

                    <ForeName>F</ForeName>

                    <Initials>B</Initials>

                </Author>

                <Author ValidYN="Y">

                    <LastName>Hodek</LastName>

                    <ForeName>C</ForeName>

                    <Initials>B</Initials>

                </Author>

            </AuthorList>

            <Language>eng</Language>

            <PublicationTypeList>

                <PublicationType>Journal Article</PublicationType>

            </PublicationTypeList>

        </Article>

        <MedlineJournalInfo>

            <Country>Slovakia</Country>

            <MedlineTA>Gen Physiol Biophys</MedlineTA>

            <NlmUniqueID>8400604</NlmUniqueID>

        </MedlineJournalInfo>

        <ChemicalList>

            <Chemical>

                <RegistryNumber>0</RegistryNumber>

                <NameOfSubstance>N-nitrosodimethylamine</NameOfSubstance>

            </Chemical>

            <Chemical>

                <RegistryNumber>0</RegistryNumber>

                <NameOfSubstance>Nitrosamines</NameOfSubstance>

            </Chemical>

            <Chemical>

                <RegistryNumber>50-06-6</RegistryNumber>

                <NameOfSubstance>Phenobarbital</NameOfSubstance>

            </Chemical>

            <Chemical>

                <RegistryNumber>614-00-6</RegistryNumber>

                <NameOfSubstance>N-methyl-N-nitrosoaniline</NameOfSubstance>

            </Chemical>

            <Chemical>

                <RegistryNumber>64-17-5</RegistryNumber>

                <NameOfSubstance>Ethanol</NameOfSubstance>

            </Chemical>

            <Chemical>

                <RegistryNumber>9035-51-2</RegistryNumber>

                <NameOfSubstance>Cytochrome P-450 Enzyme System</NameOfSubstance>

            </Chemical>

        </ChemicalList>

        <CitationSubset>I</CitationSubset>

        <MeshHeadingList>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Animals</DescriptorName>

            </MeshHeading>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Cytochrome P-450 Enzyme System</DescriptorName>

                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>

            </MeshHeading>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Ethanol</DescriptorName>

                <QualifierName MajorTopicYN="Y">administration &amp; dosage</QualifierName>

            </MeshHeading>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Liver</DescriptorName>

                <QualifierName MajorTopicYN="N">drug effects</QualifierName>

                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>

            </MeshHeading>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Male</DescriptorName>

            </MeshHeading>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Microsomes, Liver</DescriptorName>

                <QualifierName MajorTopicYN="N">drug effects</QualifierName>

                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>

            </MeshHeading>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Nitrosamines</DescriptorName>

                <QualifierName MajorTopicYN="Y">metabolism</QualifierName>

            </MeshHeading>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Phenobarbital</DescriptorName>

                <QualifierName MajorTopicYN="Y">administration &amp; dosage</QualifierName>

            </MeshHeading>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Rabbits</DescriptorName>

            </MeshHeading>

            <MeshHeading>

                <DescriptorName MajorTopicYN="N">Research Support, Non-U.S. Govt</DescriptorName>

            </MeshHeading>

        </MeshHeadingList>

    </MedlineCitation>

    <PubmedData>

        <History>

            <PubMedPubDate PubStatus="pubmed">

                <Year>2005</Year>

                <Month>4</Month>

                <Day>9</Day>

                <Hour>9</Hour>

                <Minute>0</Minute>

            </PubMedPubDate>

            <PubMedPubDate PubStatus="medline">

                <Year>2005</Year>

                <Month>8</Month>

                <Day>30</Day>

                <Hour>9</Hour>

                <Minute>0</Minute>

            </PubMedPubDate>

        </History>

        <PublicationStatus>ppublish</PublicationStatus>

        <ArticleIdList>

            <ArticleId IdType="pubmed">15815077</ArticleId>

        </ArticleIdList>

    </PubmedData>

  </PubmedArticle>

 </PubmedArticleSet>

 

=cut