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Bio::DB::Biblio::eutils.3pm

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:

   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)