#!/usr/bin/perl =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>Kubícková</LastName> <ForeName>B</ForeName> <Initials>B</Initials> </Author> <Author ValidYN="Y"> <LastName>Máslová</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