Bio-Biblio
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lib/Bio/DB/Biblio/eutils.pm view on Meta::CPAN
my $self = shift;
return $self->{'count'} = shift if @_;
return $self->{'count'};
}
sub query_key {
my $self = shift;
return $self->{'query_key'} = shift if @_;
return $self->{'query_key'};
}
1;
__END__
=pod
=encoding utf-8
=head1 NAME
Bio::DB::Biblio::eutils - access to PubMed's bibliographic query service
=head1 VERSION
version 1.70
=head1 SYNOPSIS
Do not use this object directly, it is recommended to access it and use
it through the I<Bio::Biblio> module:
use Bio::Biblio;
use Bio::Biblio::IO;
my $biblio = Bio::Biblio->new( -access => 'eutils' );
$biblio->find("10336996");
my $xml = $biblio->get_next;
my $io = Bio::Biblio::IO->new( -data => $xml,
-format => 'medlinexml' );
my $article = $io->next_bibref();
The main documentation details are to be found in
L<Bio::DB::BiblioI>.
=head1 ATTRIBUTES
=head2 db
Title : db
Usage : $obj->db($newval)
Function: specifies the database to search. valid values are:
pubmed, pmc, journals
it is also possible to add the following, and i will do
so on request:
genome, nucleotide, protein, popset, snp, sequence, taxonomy
pubmed is default.
Returns : value of db (a scalar)
Args : on set, new value (a scalar or undef, optional)
=head2 has_next
Title : has_next
Usage : $has_next = $biblio->has_next();
Function: check to see if there are more items to be retrieved
Returns : 1 on true, undef on false
Args : none
=head1 METHODS
=head2 get_collection_id
Title : get_collection_id
Usage : $id = $biblio->get_collection_id();
Function: returns WebEnv value from ESearch
Returns : ESearch WebEnv value as a string
Args : none
=head2 reset_retrieval
Title : reset_retrieval
Usage : $biblio->reset_retrieval();
Function: reset cursor in id list, see cursor()
Returns : 1
Args : none
=head2 get_next
Title : get_next
Usage : $xml = $biblio->get_next();
Function: return next record as xml
Returns : an xml string
Args : none
=head2 get_more
Title : get_more
Usage : $xml = $biblio->get_more($more);
Function: returns next $more records concatenated
Returns : a string containing multiple xml documents
Args : an integer representing how many records to retrieve
=head2 find
Title : find
Usage : $biblio = $biblio->find($pubmed_query_phrase);
Function: perform a PubMed query using Entrez ESearch
Returns : a reference to the object on which the method was called
Args : a PubMed query phrase. See
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
for help on how to construct a query.
=head2 get_all_ids
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