/ 
BioPerl-1.6.901
River stage two • 60 direct dependents • 65 total dependents
/ Bio::DB::Biblio::eutils

NAME

Bio::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:

https://redmine.open-bio.org/projects/bioperl/

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)