Bio::DB::Biblio::eutilUser Contributed Perl DocumentBio::DB::Biblio::eutils(3)NAMEBio::DB::Biblio::eutils - Access to PubMed's bibliographic query
service
SYNOPSIS
Do not use this object directly, it is recommended to access it and use
it through the 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();
DESCRIPTION
This object contains the real implementation of a Bibliographic Query
Service as defined in Bio::DB::BiblioI.
Bio::DB::BiblioI is not implemented as documented in the interface,
particularly the find() method, which is not compatible with PubMed's
query language.
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Support
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly address
it. Please include a thorough description of the problem with code and
data examples if at all possible.
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR
Allen Day <allenday@ucla.edu>
COPYRIGHT
Copyright (c) 2004 Allen Day, University of California, Los Angeles.
This module is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
DISCLAIMER
This software is provided "as is" without warranty of any kind.
BUGS AND LIMITATIONS
· More testing and debugging needed to ensure that returned citations
are properly transferred even if they contain foreign characters.
· Maximum record count (MAX_RECORDS) returned currently hard coded to
100K.
· Biblio retrieval methods should be more tightly integrated with
Bio::Biblio::Ref and Bio::DB::MeSH.
SEE ALSO
Pub Med Help:
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/help/pmhelp.html
Entrez Utilities:
http://eutils.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
Example code:
examples/biblio/biblio-eutils-example.pl
APPENDIX
The main documentation details are to be found in Bio::DB::BiblioI.
Here is the rest of the object methods. Interface methods first,
followed by internal methods.
_initialize
Usage : my $obj = Bio::Biblio->new(-access => 'eutils' ...);
(_initialize is internally called from this constructor)
Returns : 1 on success
Args : none
This is an actual new() method (except for the real object creation and
its blessing which is done in the parent class Bio::Root::Root in
method _create_object).
Note that this method is called always as an object method (never as a
class method) - and that the object who calls this method may already
be partly initiated (from Bio::Biblio::new method); so if you need to
do some tricks with the 'class invocation' you need to change
Bio::Biblio::new method, not this one.
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)
Methods implementing Bio::DB::BiblioI interface
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
reset_retrieval
Title : reset_retrieval
Usage : $biblio->reset_retrieval();
Function: reset cursor in id list, see cursor()
Returns : 1
Args : none
get_next
Title : get_next
Usage : $xml = $biblio->get_next();
Function: return next record as xml
Returns : an xml string
Args : none
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
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
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.
get_all_ids
Title : get_all_ids
Usage : @ids = $biblio->get_all_ids();
Function: return a list of PubMed ids resulting from call to find()
Returns : a list of PubMed ids, or an empty list
Args : none
get_all
Title : get_all
Usage : $xml = $biblio->get_all();
Function: retrieve all records from query
Returns : return a large concatenated string of PubMed xml documents
Args : none
exists
Title : exists
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
destroy
Title : destroy
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
get_vocabulary_names
Title : get_vocabulary_names
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : empty arrayref
Args : none
contains
Title : contains
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
get_entry_description
Title : get_entry_description
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
get_all_values
Title : get_all_values
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
get_all_entries
Title : get_all_entries
Usage : do not use
Function: no-op. this is here only for interface compatibility
Returns : undef
Args : none
Internal methods unrelated to Bio::DB::BiblioI
cursor
Title : cursor
Usage : $obj->cursor($newval)
Function: holds position in reference collection
Returns : value of cursor (a scalar)
Args : on set, new value (a scalar or undef, optional)
twig
Title : twig
Usage : $obj->twig($newval)
Function: holds an XML::Twig instance.
Returns : value of twig (a scalar)
Args : on set, new value (a scalar or undef, optional)
ids
Title : ids
Usage : $obj->ids($newval)
Function: store pubmed ids resulting from find() query
Returns : value of ids (a scalar)
Args : on set, new value (a scalar or undef, optional)
collection_id
Title : collection_id
Usage : $obj->collection_id($newval)
Function:
Returns : value of collection_id (a scalar)
Args : on set, new value (a scalar or undef, optional)
count
Title : count
Usage : $obj->count($newval)
Function:
Returns : value of count (a scalar)
Args : on set, new value (a scalar or undef, optional)
query_key
Title : query_key
Usage : $obj->query_key($newval)
Function: holds query_key from ESearch document
Returns : value of query_key (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.14.1 2011-07-22 Bio::DB::Biblio::eutils(3)
