#!/usr/bin/perl
use utf8;
=encoding utf-8
=head1 NAME
biblio-eutils.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>KubE<237>ckovE<225></LastName>
<ForeName>B</ForeName>
<Initials>B</Initials>
</Author>
<Author ValidYN="Y">
<LastName>ME<225>slovE<225></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 & 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 & 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