Provided by: libbio-perl-perl_1.6.901-2_all bug

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)